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Hani Goodarzi, PhD

TitleAssistant Professor
InstitutionUniversity of California San Francisco
DepartmentBiochemistry and Biophysics
Address600 16th St
San Francisco CA 94158
Phone415-230-5189
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    Collapse Biography 
    Collapse Education and Training
    Rockefeller University, New YorkPostdoctoral04/2016Cancer Systems Biology
    Princeton, New JerseyPhD10/2010Computational Biology & Genomics
    Collapse Awards and Honors
    2017AAAS Martin and Rose Wachtel Cancer Research Award
    2017AACR NextGen Award for Transformative Cancer Research
    2017Sidney Kimmel Cancer Foundation Scholar Award
    2015Blavatnik Regional Awards for Young Scientists
    2015Tri-Institutional Breakout Prize for Junior Investigators

    Collapse Overview 
    Collapse Overview
    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.


    Collapse Research 
    Collapse Research Activities and Funding
    Targeted regulation of transcript stability through RNA methylation and intron retention
    NIH R01GM123977Sep 1, 2017 - Aug 31, 2022
    Role: Principal Investigator
    Systematic dissection of an aberrant splicing program driving cancer metastasis
    NIH R00CA194077May 1, 2016 - Apr 30, 2019
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Fish L, Zhang S, Yu JX, Culbertson B, Zhou AY, Goga A, Goodarzi H. Cancer cells exploit an orphan RNA to drive metastatic progression. Nat Med. 2018 Nov; 24(11):1743-1751. PMID: 30397354.
      View in: PubMed
    2. Alkallas R, Fish L, Goodarzi H, Najafabadi HS. Publisher Correction: Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease. Nat Commun. 2018 Oct 31; 9(1):4625. PMID: 30382106.
      View in: PubMed
    3. Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 2018 Oct 18; 175(3):889. PMID: 30340047.
      View in: PubMed
    4. Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 2018 Jul 17. PMID: 30033370.
      View in: PubMed
    5. Knott SRV, Wagenblast E, Khan S, Kim SY, Soto M, Wagner M, Turgeon MO, Fish L, Erard N, Gable AL, Maceli AR, Dickopf S, Papachristou EK, D'Santos CS, Carey LA, Wilkinson JE, Harrell JC, Perou CM, Goodarzi H, Poulogiannis G, Hannon GJ. Erratum: Asparagine bioavailability governs metastasis in a model of breast cancer. Nature. 2018 Apr 04; 556(7699):135. PMID: 29620732.
      View in: PubMed
    6. Knott SRV, Wagenblast E, Khan S, Kim SY, Soto M, Wagner M, Turgeon MO, Fish L, Erard N, Gable AL, Maceli AR, Dickopf S, Papachristou EK, D'Santos CS, Carey LA, Wilkinson JE, Harrell JC, Perou CM, Goodarzi H, Poulogiannis G, Hannon GJ. Asparagine bioavailability governs metastasis in a model of breast cancer. Nature. 2018 Feb 15; 554(7692):378-381. PMID: 29414946.
      View in: PubMed
    7. Alkallas R, Fish L, Goodarzi H, Najafabadi HS. Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease. Nat Commun. 2017 10 13; 8(1):909. PMID: 29030541.
      View in: PubMed
    8. Bukowski R, Sadovsky Y, Goodarzi H, Zhang H, Biggio JR, Varner M, Parry S, Xiao F, Esplin SM, Andrews W, Saade GR, Ilekis JV, Reddy UM, Baldwin DA. Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface. PeerJ. 2017; 5:e3685. PMID: 28879060.
      View in: PubMed
    9. Goodarzi H. Charting the "unknown unknowns" of cancer progression. Sci Transl Med. 2017 Jul 26; 9(400). PMID: 28747512.
      View in: PubMed
    10. Kingham TP, Nguyen HCB, Zheng J, Konstantinidis IT, Sadot E, Shia J, Kuk D, Zhang S, Saltz L, D'Angelica MI, Jarnagin WR, Goodarzi H, Tavazoie SF. MicroRNA-203 predicts human survival after resection of colorectal liver metastasis. Oncotarget. 2017 Mar 21; 8(12):18821-18831. PMID: 27935861.
      View in: PubMed
    11. Lee H, Goodarzi H, Tavazoie SF, Alarcón CR. TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer. Cancer Res. 2016 09 01; 76(17):4994-5005. PMID: 27328729.
      View in: PubMed
    12. Goodarzi H, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF. Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. Cell. 2016 Jun 02; 165(6):1416-1427. PMID: 27259150; PMCID: PMC4915377 [Available on 06/02/17].
      View in: PubMed, PubMed Central
    13. Nguyen A, Yoshida M, Goodarzi H, Tavazoie SF. Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness. Nat Commun. 2016 May 03; 7:11246. PMID: 27138336; PMCID: PMC4857405.
      View in: PubMed, PubMed Central
    14. Hwang HW, Park CY, Goodarzi H, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB. PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage. Cell Rep. 2016 Apr 12; 15(2):423-35. PMID: 27050522; PMCID: PMC4832608.
      View in: PubMed, PubMed Central
    15. Fish L, Pencheva N, Goodarzi H, Tran H, Yoshida M, Tavazoie SF. Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts. Genes Dev. 2016 Feb 15; 30(4):386-98. PMID: 26883358; PMCID: PMC4762424.
      View in: PubMed, PubMed Central
    16. Alarcón CR, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF. HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events. Cell. 2015 Sep 10; 162(6):1299-308. PMID: 26321680; PMCID: PMC4673968.
      View in: PubMed, PubMed Central
    17. Furlow PW, Zhang S, Soong TD, Halberg N, Goodarzi H, Mangrum C, Wu YG, Elemento O, Tavazoie SF. Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival. Nat Cell Biol. 2015 Jul; 17(7):943-52. PMID: 26098574.
      View in: PubMed
    18. Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF. Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell. 2015 May 07; 161(4):790-802. PMID: 25957686; PMCID: PMC4457382.
      View in: PubMed, PubMed Central
    19. Alarcón CR, Lee H, Goodarzi H, Halberg N, Tavazoie SF. N6-methyladenosine marks primary microRNAs for processing. Nature. 2015 Mar 26; 519(7544):482-5. PMID: 25799998; PMCID: PMC4475635.
      View in: PubMed, PubMed Central
    20. Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF. Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature. 2014 Sep 11; 513(7517):256-60. PMID: 25043050; PMCID: PMC4440807.
      View in: PubMed, PubMed Central
    21. Oikonomou P, Goodarzi H, Tavazoie S. Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts. Cell Rep. 2014 Apr 10; 7(1):281-92. PMID: 24656821; PMCID: PMC4430845.
      View in: PubMed, PubMed Central
    22. Goodarzi H, Tavazoie SF, Tavazoie S. TARBP2 binding structured RNA elements drives metastasis. Cell Cycle. 2014; 13(18):2799-800. PMID: 25486461; PMCID: PMC4612561.
      View in: PubMed, PubMed Central
    23. Freddolino PL, Goodarzi H, Tavazoie S. Revealing the genetic basis of natural bacterial phenotypic divergence. J Bacteriol. 2014 Feb; 196(4):825-39. PMID: 24317396; PMCID: PMC3911184.
      View in: PubMed, PubMed Central
    24. Chiu IM, Morimoto ET, Goodarzi H, Liao JT, O'Keeffe S, Phatnani HP, Muratet M, Carroll MC, Levy S, Tavazoie S, Myers RM, Maniatis T. A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep. 2013 Jul 25; 4(2):385-401. PMID: 23850290; PMCID: PMC4272581.
      View in: PubMed, PubMed Central
    25. Freddolino PL, Goodarzi H, Tavazoie S. Fitness landscape transformation through a single amino acid change in the rho terminator. PLoS Genet. 2012 May; 8(5):e1002744. PMID: 22693458; PMCID: PMC3364947.
      View in: PubMed, PubMed Central
    26. Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S. Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature. 2012 Apr 08; 485(7397):264-8. PMID: 22495308; PMCID: PMC3350620.
      View in: PubMed, PubMed Central
    27. Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celià-Terrassa T, Mercatali L, Khan Z, Goodarzi H, Hua Y, Wei Y, Hu G, Garcia BA, Ragoussis J, Amadori D, Harris AL, Kang Y. Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nat Med. 2011 Aug 07; 17(9):1101-8. PMID: 21822286.
      View in: PubMed
    28. Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S. Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol. 2010 Jun 08; 6:378. PMID: 20531407; PMCID: PMC2913397.
      View in: PubMed, PubMed Central
    29. Goodarzi H, Elemento O, Tavazoie S. Revealing global regulatory perturbations across human cancers. Mol Cell. 2009 Dec 11; 36(5):900-11. PMID: 20005852; PMCID: PMC2900319.
      View in: PubMed, PubMed Central
    30. Najafabadi HS, Goodarzi H, Salavati R. Universal function-specificity of codon usage. Nucleic Acids Res. 2009 Nov; 37(21):7014-23. PMID: 19773421; PMCID: PMC2790905.
      View in: PubMed, PubMed Central
    31. Goodarzi H, Hottes AK, Tavazoie S. Global discovery of adaptive mutations. Nat Methods. 2009 Aug; 6(8):581-3. PMID: 19597501; PMCID: PMC2762608.
      View in: PubMed, PubMed Central
    32. Amini S, Goodarzi H, Tavazoie S. Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli. PLoS Pathog. 2009 May; 5(5):e1000432. PMID: 19436718; PMCID: PMC2675270.
      View in: PubMed, PubMed Central
    33. Goodarzi H, Torabi N, Najafabadi HS, Archetti M. Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons. Gene. 2008 Jan 15; 407(1-2):30-41. PMID: 17977670.
      View in: PubMed
    34. Elahi E, Shafaghati Y, Asadi S, Absalan F, Goodarzi H, Gharaii N, Karimi-Nejad MH, Shahram F, Hughes AE. Intragenic SNP haplotypes associated with 84dup18 mutation in TNFRSF11A in four FEO pedigrees suggest three independent origins for this mutation. J Bone Miner Metab. 2007; 25(3):159-64. PMID: 17447113.
      View in: PubMed
    35. Goodarzi H, Katanforoush A, Torabi N, Najafabadi HS. Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix. J Theor Biol. 2007 Apr 21; 245(4):715-25. PMID: 17240399.
      View in: PubMed
    36. Torabi N, Goodarzi H, Shateri Najafabadi H. The case for an error minimizing set of coding amino acids. J Theor Biol. 2007 Feb 21; 244(4):737-44. PMID: 17069856.
      View in: PubMed
    37. Marashi SA, Goodarzi H, Sadeghi M, Eslahchi C, Pezeshk H. Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. Comput Biol Chem. 2006 Feb; 30(1):50-7. PMID: 16386465.
      View in: PubMed
    38. Goodarzi H, Najafabadi HS, Nejad HA, Torabi N. The impact of including tRNA content on the optimality of the genetic code. Bull Math Biol. 2005 Nov; 67(6):1355-68. PMID: 16005951.
      View in: PubMed
    39. Goodarzi H, Shateri Najafabadi H, Torabi N. On the coevolution of genes and genetic code. Gene. 2005 Dec 05; 362:133-40. PMID: 16213111.
      View in: PubMed
    40. Goodarzi H, Najafabadi HS, Hassani K, Nejad HA, Torabi N. On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. J Theor Biol. 2005 Aug 07; 235(3):318-25. PMID: 15882694.
      View in: PubMed
    41. Najafabadi HS, Goodarzi H, Torabi N, Banihosseini SS. Applying a neural network to predict the thermodynamic parameters for an expanded nearest-neighbor model. J Theor Biol. 2006 Feb 07; 238(3):657-65. PMID: 16061260.
      View in: PubMed
    42. Goodarzi H, Najafabadi HS, Torabi N. Designing a neural network for the constraint optimization of the fitness functions devised based on the load minimization of the genetic code. Biosystems. 2005 Aug; 81(2):91-100. PMID: 15936137.
      View in: PubMed
    43. Najafabadi HS, Goodarzi H, Torabi N. Optimality of codon usage in Escherichia coli due to load minimization. J Theor Biol. 2005 Nov 21; 237(2):203-9. PMID: 15932760.
      View in: PubMed
    44. Najafabadi HS, Goodarzi H. Correspondence regarding Bharanidharan et al., "Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species". Biochem Biophys Res Commun. 2004 Dec 03; 325(1):1-2. PMID: 15522192.
      View in: PubMed
    45. Goodarzi H, Nejad HA, Torabi N. On the optimality of the genetic code, with the consideration of termination codons. Biosystems. 2004 Nov; 77(1-3):163-73. PMID: 15527955.
      View in: PubMed
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