Publications

2016-present

Goodarzi H (2017). Charting the “unknown unknowns” of cancer progression. Sci Transl Med 9 (400), eaao0959.

Kingham PT, Nguyen CB, Zheng J, Konstantinidis IT, Sadot E, Shia J, Kuk D, Zhang S, Saltz L, D’Angelica M, Jarnagin WR, Goodarzi H✝, Tavazoie SF✝ (2016). MicroRNA-203 predicts human survival after resection of colorectal liver metastasis. Oncotarget 8:18821-31. ✝ Co-correspoding authors

Goodarzi H*✝, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF✝ (2016). Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell 165, 1416-1427. *Contributed equally; ✝ Co-correspoding authors

Lee H, Goodarzi H, Tavazoie SF, Alarcon CR (2016). TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer. Cancer Res 76(17):4994-5005.

Hwang HW, Park CY, Goodarzi H, 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. Cell Rep 15(2):423-435.

Nguyen A, Yoshida M, Goodarzi H, Tavazoie SF (2016). Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness. Nature Comm 7: 11246.

Fish L, Pencheva N*, Goodarzi H*, Tran H, Yoshida M, Tavazoie SF (2016). Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts. Genes & Dev 30: 386-398. *Contributed equally

2012-2015

Alarcon C, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF (2015). HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events. Cell 162: 1299-1308.

Goodarzi H, Liu X, Nguyen HCB, Fish L, Tavazoie SF (2015). Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell 161: 790-802.

Furlow PW, Zhang S, Soong ST, Halberg N, Goodarzi H, Mangrum C, Wu G, Elemento O, Tavazoie S (2015). Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival. Nature Cell Bio 17, 943-952.

Alarcon CR, Lee H*, Goodarzi H*, Halberg N, Tavazoie S (2015). N6-methyladenosine marks primary microRNAs for processing. Nature 519, 482-485. *Contributed equally

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

Oikonomou P*, Goodarzi H*, Tavazoie S (2014). Systematic Identification of Regulatory Elements in Conserved 3? UTRs of Human Transcripts. Cell Reports 7(1): 281-292. *Contributed equally

Freddolino PL*, Goodarzi H*, Tavazoie S (2013). Revealing the genetic basis of natural bacterial phenotypic divergence. J. Bacteriol. doi:10.1128/JB.01039-13 *Contributed equally

Chiu IM, Morimoto ETA, Goodarzi H, 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. Cell Reports 4(2): 385-401

Freddolino PL*, Goodarzi H*, Tavazoie S (2012). Fitness landscape transformation through a single amino acid change in the Rho terminator. PLoS Genetics Vol. 8, e1002744. *Contributed equally

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.

2007-2011

Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celia-Terrassa T, Mercatali L, Khan Z, Goodarzi H, et al. (2011). Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature Med 17(9):1048-9.

Goodarzi H, Bennet BD, et al. (2010). Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol 6:278.

Goodarzi H*, Elemento O*, Tavazoie S (2009). Revealing Global Regulatory Perturbations across Human Cancers. Mol Cell 36:900-11. *contributed equally

Najafabadi HS*, Goodarzi H*, Salavati R (2009). Universal function-specificity of codon usage. Nucl Acids Res 37(21):7014-7023. *contributed equally

Goodarzi H, Hottes AK, Tavazoie S (2009). Global discovery of adaptive mutations. Nat Methods 6(8):581-3.

Amini S, Goodarzi H, Tavazoie S (2009). Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli. PLoS Pathogens 5:e1000432.

Goodarzi H, Torabi N, Najafabadi HS, Archetti M (2008). Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons. Gene 407(1-2):30-41.

Elahi E, Shafaghati Y, Asadi S, Absalan F, Goodarzi H, et al. (2007). Intragenic SNP haplotypes associated with 84dup18 mutation in TNFRSF11A in four FEO pedigrees suggest three independent origins for this mutation. J Bone Miner Metab 25(3):159-64.

Goodarzi H, Katanforoush A, Torabi N, Najafabadi HS (2007). Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix. J Theor Biol 245(4):715-25.

Torabi N, Goodarzi H, Shateri Najafabadi H. (2007). The case for an error minimizing set of coding amino acids. J Theor Biol 244(4):737-44.

2004-2006

Najafabadi HS, Goodarzi H, Torabi N, Banihosseini SS.(2006). Applying a neural network to predict the thermodynamic parameters for an expanded nearest-neighbor model. J Theor Biol 238(3):657-65.

Marashi SA, Goodarzi H, Sadeghi M, Eslahchi C, Pezeshk H (2006). Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. Comput Biol Chem 30(1):50-7.

Goodarzi H, Shateri Najafabadi H, Torabi N (2005). On the coevolution of genes and genetic code. Gene 362:133-40.

Najafabadi HS, Goodarzi H, Torabi N (2005). Optimality of codon usage in Escherichia coli due to load minimization. J Theor Biol 237(2):203-9.

Goodarzi H, 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. J Theor Biol 235(3):318-25.

Goodarzi H, 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. Biosystems 81(2):91-100.

Goodarzi H, Nejad HA, Torabi N (2005). On the optimality of the genetic code, with the consideration of termination codons. Biosystems 77(1-3):163-73.

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