Hani Goodarzi, PhD
Associate Professor
Biochemistry and Biophysics
School of Medicine

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.

• Author Correction: Systematic identification of post-transcriptional regulatory modules.
  Nature communications 2024 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 …
• A Suite of Foundation Models Captures the Contextual Interplay Between Codons.
  bioRxiv : the preprint server for biology 2024 Naghipourfar M, Chen S, Howard MK, Macdonald CB, Saberi A, Hagen T, Mofrad MRK, Coyote-Maestas W, Goodarzi H
• Functional screen for mediators of onco-mRNA translation specificity.
  bioRxiv : the preprint server for biology 2024 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
• 261 (PB249): ENPP1 is an innate immune checkpoint of the anticancer cGAMPSTING pathway in breast cancer.
  European Journal of Cancer 2024 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
• Tumor Cell Spatial Organization Directs EGFR/RAS/RAF Pathway Primary Therapy Resistance through YAP Signaling.
  bioRxiv : the preprint server for biology 2024 Nakagawa R, Beardsley A, Durney S, Hayward MK, Subramanyam V, Meyer NP, Wismer H, Goodarzi H, Weaver VM, Van de Mark D, Goga A
• Abstract A078: Functional screen for mediators of onco-mRNA translation specificity in pancreatic cancer.
  Cancer Research 2024 Joanna R Kovalski, Goksu Sarioglu, Vishvak Subramanyam, Grace Hernandez, Gilles Rademaker, Juan A Oses-Prieto, Macey Slota, Kwun Wah Wen, Grace E Kim, Alma L Burlingame, Hani Goodarzi, Rushika M …
• Learning chemical sensitivity reveals mechanisms of cellular response.
  Communications biology 2024 Connell W, Garcia K, Goodarzi H, Keiser MJ
• Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.
  Cell reports 2024 Woo BJ, Moussavi-Baygi R, Karner H, Karimzadeh M, Yousefi H, Lee S, Garcia K, Joshi T, Yin K, Navickas A, Gilbert LA, Wang B, Asgharian H, Feng FY, Goodarzi H
• Systematic identification of post-transcriptional regulatory modules.
  Nature communications 2024 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 …
• pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease.
  PLoS computational biology 2024 Bakulin A, Teyssier NB, Kampmann M, Khoroshkin M, Goodarzi H
• Identifying a gene signature of metastatic potential by linking pre-metastatic state to ultimate metastatic fate.
  bioRxiv : the preprint server for biology 2024 Handler JS, Li Z, Dveirin RK, Fang W, Goodarzi H, Fertig EJ, Kalhor R
• RPL22 is a tumor suppressor in MSI-high cancers and a splicing regulator of MDM4.
  Cell reports 2024 Weinstein HNW, Hu K, Fish L, Chen YA, Allegakoen P, Pham JH, Hui KSF, Chang CH, Tutar M, Benitez-Rivera L, Baco MB, Song H, Giacomelli AO, Vazquez F, Ghandi M, Goodarzi H, Huang FW
• Glycosphingolipid synthesis mediates immune evasion in KRAS-driven cancer.
  Nature 2024 Soula M, Unlu G, Welch R, Chudnovskiy A, Uygur B, Shah V, Alwaseem H, Bunk P, Subramanyam V, Yeh HW, Khan A, Heissel S, Goodarzi H, Victora GD, Beyaz S, Birsoy K
• A systematic search for RNA structural switches across the human transcriptome.
  Nature methods 2024 Khoroshkin M, Asarnow D, Zhou S, Navickas A, Winters A, Goudreau J, Zhou SK, Yu J, Palka C, Fish L, Borah A, Yousefi K, Carpenter C, Ansel KM, Cheng Y, Gilbert LA, Goodarzi H
• Accurate isoform quantification by joint short- and long-read RNA-sequencing.
  bioRxiv : the preprint server for biology 2024 Apostolides M, Choi B, Navickas A, Saberi A, Soto LM, Goodarzi H, Najafabadi HS
• High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors.
  bioRxiv : the preprint server for biology 2024 Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL
• Effect of breast tissue density on cell-free orphan non-coding RNAs secreted by breast cancers.
  Journal of Clinical Oncology 2024 Jeremy Ku, Akshaya Krishnan, Kim Hue Mai, Alice Huang, Dang D Nguyen, Selina Chen, Rose Hanna, Noura Tbeileh, Jieyang Wang, Xuan Zhao, Nae-Chyun Chen, Helen Li, Anna Hartwig, Fereydoun Hormozdiari, …
• Harnessing cell-free orphan non-coding RNAs as a predictive measure of long-term survival in neoadjuvant breast cancer therapy.
  Journal of Clinical Oncology 2024 Taylor B. Cavazos, Mehran Karimzadeh, Amir Momen-Roknabadi, Gillian L. Hirst, Lamorna Brown Swigart, Christina Yau, Dang Nguyen, Alice Huang, Selina Chen, Rose Hanna, Akshaya Krishnan, Anna Hartwig, …
• Stem-cell states converge in multistage cutaneous squamous cell carcinoma development.
  Science (New York, N.Y.) 2024 Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A
• Identification of the extracellular membrane protein ENPP3 as a major cGAMP hydrolase and innate immune checkpoint.
  Cell reports 2024 Mardjuki R, Wang S, Carozza J, Zirak B, Subramanyam V, Abhiraman G, Lyu X, Goodarzi H, Li L
• Direct transposition of native DNA for sensitive multimodal single-molecule sequencing.
  Nature genetics 2024 Nanda AS, Wu K, Irkliyenko I, Woo B, Ostrowski MS, Clugston AS, Sayles LC, Xu L, Satpathy AT, Nguyen HG, Alejandro Sweet-Cordero E, Goodarzi H, Kasinathan S, Ramani V
• Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer.
  Nature communications 2024 Haderk F, Chou YT, Cech L, Fernández-Méndez C, Yu J, Olivas V, Meraz IM, Barbosa Rabago D, Kerr DL, Gomez C, Allegakoen DV, Guan J, Shah KN, Herrington KA, Gbenedio OM, Nanjo S, Majidi M, Tamaki W, …
• Abstract PO2-13-08: Cell-free orphan noncoding RNAs and AI enable early detection of invasive breast cancer and ductal carcinoma in-situ.
  Cancer Research 2024 Noura Tbeileh, Taylor Cavazos, Mehran Karimzadeh, Jeffrey Wang, Alice Huang, Dung Ngoc Lam, Seda Kilinc, Jieyang Wang, Xuan Zhao, Andy Pohl, Helen Li, Lisa Fish, Kimberly Chau, Marra Francis, Lee …
• Abstract 1256: RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4.
  Cancer Research 2024 Hannah N. Weinstein, Kevin Hu, Lisa Fish, Yih-An Chen, Paul Allegakoen, Keliana S. Hui, Julia H. Pham, Maria B. Baco, Hanbing Song, Andrew O. Giacomelli, Francisca Vazquez, Mahmoud Ghandi3, Hani …
• Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.
  bioRxiv : the preprint server for biology 2024 Wang J, Suh JM, Woo BJ, Navickas A, Garcia K, Yin K, Fish L, Cavazos T, Hänisch B, Markett D, Yu S, Hirst G, Brown-Swigart L, Esserman LJ, van 't Veer LJ, Goodarzi H
• Revealing the grammar of small RNA secretion using interpretable machine learning.
  Cell genomics 2024 Zirak B, Naghipourfar M, Saberi A, Pouyabahar D, Zarezadeh A, Luo L, Fish L, Huh D, Navickas A, Sharifi-Zarchi A, Goodarzi H
• Translational adaptation in breast cancer metastasis and emerging therapeutic opportunities.
  Trends in pharmacological sciences 2024 Chen S, Navickas A, Goodarzi H
• Functional microRNA-targeting drug discovery by graph-based deep learning.
  Patterns (New York, N.Y.) 2024 Keshavarzi Arshadi A, Salem M, Karner H, Garcia K, Arab A, Yuan JS, Goodarzi H
• Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis.
  bioRxiv : the preprint server for biology 2024 Sun N, Teyssier N, Wang B, Drake S, Seyler M, Zaltsman Y, Everitt A, Teerikorpi N, Willsey HR, Goodarzi H, Tian R, Kampmann M, Willsey AJ
• Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms.
  bioRxiv : the preprint server for biology 2023 McKeever PM, Sababi AM, Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, Bader GD, Robertson…
• ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway in breast cancer.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Wang S, Böhnert V, Joseph AJ, Sudaryo V, Skariah G, Swinderman JT, Yu FB, Subramanyam V, Wolf DM, Lyu X, Gilbert LA, Van't Veer LJ, Goodarzi H, Li L
• RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4.
  bioRxiv : the preprint server for biology 2023 Weinstein HNW, Hu K, Fish L, Chen YA, Allegakoen P, Hui KSF, Pham JH, Baco MB, Song H, Giacomelli AO, Vazquez F, Ghandi M, Goodarzi H, Huang FW
• Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler.
  Nature structural & molecular biology 2023 Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V
• Learning chemical sensitivity reveals mechanisms of cellular response.
  bioRxiv : the preprint server for biology 2023 Connell W, Garcia K, Goodarzi H, Keiser MJ
• Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes.
  Frontiers in oncology 2023 Yu K, Basu A, Yau C, Wolf DM, Goodarzi H, Bandyopadhyay S, Korkola JE, Hirst GL, Asare S, DeMichele A, Hylton N, Yee D, Esserman L, van 't Veer L, Sirota M
• ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway.
  bioRxiv : the preprint server for biology 2023 Wang S, Böhnert V, Joseph AJ, Sudaryo V, Swinderman J, Yu FB, Lyu X, Skariah G, Subramanyam V, Gilbert LA, Goodarzi H, Lingyin L
• Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.
  bioRxiv : the preprint server for biology 2023 Woo BJ, Moussavi-Baygi R, Karner H, Karimzadeh M, Garcia K, Joshi T, Yin K, Navickas A, Gilbert LA, Wang B, Asgharian H, Feng FY, Goodarzi H
• A bi-steric mTORC1-selective inhibitor overcomes drug resistance in breast cancer.
  Oncogene 2023 Meng D, Zhao X, Yang YC, Navickas A, Helland C, Goodarzi H, Singh M, Bandyopadhyay S
• Consensus molecular subtypes and orphan non-coding RNAs in colorectal cancer.
  Journal of Clinical Oncology 2023 Jeffrey Wang, Mehran Karimzadeh, Taylor B. Cavazos, Afsaneh Barzi, Kathleen Wang, Rose Hanna, Patrick Arensdorf, Kimberly H. Chau, Helen Li, Hani Goodarzi, Lisa Fish, Fereydoun Hormozdiari, Babak …
• Detection of early-stage cancers using circulating orphan non-coding RNAs in blood.
  Journal of Clinical Oncology 2023 Mehran Karimzadeh, Jeffrey Wang, Taylor B. Cavazos, Lee S. Schwartzberg, Michael Multhaup, Jeremy Ku, Xuan Zhao, Jieyang Wang, Kathleen Wang, Rose Hanna, Patrick Arensdorf, Kimberly H Chau, Helen Li, …
• A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression.
  Nature cancer 2023 Culbertson B, Garcia K, Markett D, Asgharian H, Chen L, Fish L, Navickas A, Yu J, Woo B, Nanda AS, Choi B, Zhou S, Rabinowitz J, Goodarzi H
• 7SK methylation by METTL3 promotes transcriptional activity.
  Science advances 2023 Perez-Pepe M, Desotell AW, Li H, Li W, Han B, Lin Q, Klein DE, Liu Y, Goodarzi H, Alarcón CR
• Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis.
  bioRxiv : the preprint server for biology 2023 Taylor MA, Kandyba E, Halliwill K, Delrosario R, Koroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam S, Mirzoeva O, Akhurst RJ, Balmain A
• An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus.
  Nature cell biology 2023 Navickas A, Asgharian H, Winkler J, Fish L, Garcia K, Markett D, Dodel M, Culbertson B, Miglani S, Joshi T, Yin K, Nguyen P, Zhang S, Stevers N, Hwang HW, Mardakheh F, Goga A, Goodarzi H
• Deriving Schwann cells from hPSCs enables disease modeling and drug discovery for diabetic peripheral neuropathy.
  Cell stem cell 2023 Majd H, Amin S, Ghazizadeh Z, Cesiulis A, Arroyo E, Lankford K, Majd A, Farahvashi S, Chemel AK, Okoye M, Scantlen MD, Tchieu J, Calder EL, Le Rouzic V, Shibata B, Arab A, Goodarzi H, Pasternak G, …
• Abstract LB170: Artificial intelligence-assisted morphology-based detection and enrichment of malignant effusion tumor cells as a method for molecular profiling.
  Cancer Research 2023 Mark J. Magbanua, Laura Huppert, Janifer Cruz, Jackson Goudreau, Shaopu Zhou, Keyi Yin, Pavel Stejskal, Ryan Carelli, Julie Kim, Linda Hsie, Maggie Wang, Zhouyang Lian, Michael Phelan, Manisha Ray, …
• Abstract 5711: Blood-based early detection of non-small cell lung cancer using orphan noncoding RNAs.
  Cancer Research 2023 Mehran Karimzadeh, Jeffrey Wang, Aiden Sababi, Oluwadamilare I. Afolabi, Dung Ngoc Lam, Alice Huang, Diana R. Corti, Kristle C. Garcia, Seda Kilinc, Xuan Zhao, Jieyang Wang, Taylor B. Cavazos, Patrick…
• Propagated Circulating Tumor Cells Uncover the Potential Role of NFκB, EMT, and TGFβ Signaling Pathways and COP1 in Metastasis.
  Cancers 2023 Xiao J, Sharma U, Arab A, Miglani S, Bhalla S, Suguru S, Suter R, Mukherji R, Lippman ME, Pohlmann PR, Zeck JC, Marshall JL, Weinberg BA, He AR, Noel MS, Schlegel R, Goodarzi H, Agarwal S
• The molecular consequences of androgen activity in the human breast.
  Cell genomics 2023 Raths F, Karimzadeh M, Ing N, Martinez A, Yang Y, Qu Y, Lee TY, Mulligan B, Devkota S, Tilley WT, Hickey TE, Wang B, Giuliano AE, Bose S, Goodarzi H, Ray EC, Cui X, Knott SRV
• Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma.
  bioRxiv : the preprint server for biology 2023 Samuel RM, Navickas A, Maynard A, Gaylord EA, Garcia K, Bhat S, Majd H, Richter MN, Elder N, Le D, Nguyen P, Shibata B, Llabata ML, Selleri L, Laird DJ, Darmanis S, Goodarzi H, Fattahi F
• Abstract P1-05-18: Orphan non-coding RNAs for early detection of breast cancer with liquid biopsy.
  Cancer Research 2023 Taylor B. Cavazos, Jeffrey Wang, Oluwadamilare I. Afolabi, Alice Huang, Dung Ngoc Lam, Seda Kilinc, Jieyang Wang, Lisa Fish, Xuan Zhao, Andy Pohl, Helen Li, Kimberly H. Chau, Patrick A. Arensdorf, …
• SYF2 suppression mitigates neurodegeneration in models of diverse forms of ALS.
  Cell stem cell 2023 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…
• Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance.
  Molecular cancer 2023 Stejskal P, Goodarzi H, Srovnal J, Hajdúch M, van 't Veer LJ, Magbanua MJM
• Functional microRNA-Targeting Drug Discovery by Graph-Based Deep Learning.
  bioRxiv : the preprint server for biology 2023 Arshadi AK, Salem M, Karner H, Garcia K, Arab A, Yuan JS, Goodarzi H
• Two isoleucyl tRNAs that decode synonymous codons divergently regulate breast cancer metastatic growth by controlling translation of proliferation-regulating genes.
  Nature cancer 2022 Earnest-Noble LB, Hsu D, Chen S, Asgharian H, Nandan M, Passarelli MC, Goodarzi H, Tavazoie SF
• 95P Serum-based colorectal cancer detection using orphan noncoding RNAs.
  Annals of Oncology 2022 H. Goodarzi, J. Wang, O. Afolabi, L. Fish, H. Li, K. Chau, P. Arensdorf, F. Hormozdiari, B. Alipanahi
• PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity.
  Scientific reports 2022 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, Goodarzi H, Goodison S, Rosser CJ
• Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling.
  Stem cell reviews and reports 2022 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, Goodarzi H, Seeley WW, Kao AW
• Abstract 3353: Discovery and validation of orphan noncoding RNA profiles across multiple cancers in TCGA and two independent cohorts.
  Cancer Research 2022 Jeffrey Wang, Helen Li, Lisa Fish, Kimberly H. Chau, Patrick Arensdorf, Hani Goodarzi, Babak Alipanahi
• Identifying drivers of breast cancer metastasis in progressively invasive subpopulations of zebrafish-xenografted MDA-MB-231.
  Molecular biomedicine 2022 Xiao J, McGill JR, Nasir A, Lekan A, Johnson B, Wilkins DJ, Pearson GW, Tanner K, Goodarzi H, Glasgow E, Schlegel R, Agarwal S
• Leucyl-tRNA synthetase is a tumour suppressor in breast cancer and regulates codon-dependent translation dynamics.
  Nature cell biology 2022 Passarelli MC, Pinzaru AM, Asgharian H, Liberti MV, Heissel S, Molina H, Goodarzi H, Tavazoie SF
• Abstract PD9-04: Tumor-released circulating orphan non-coding RNAs reflect treatment response and survival in breast cancer.
  Cancer Research 2022 Hani Goodarzi, Albertas Navickas, Jefferey Wang, Kristle Garcia, Mark J Magbanua, Lisa Fish, Lamorna Brown Swigart, Gillian Hirst, Denise Wolf, Christina Yau, Jo Chien, Carol Simmons, Amy Delson, …
• C/EBPB-dependent adaptation to palmitic acid promotes tumor formation in hormone receptor negative breast cancer.
  Nature communications 2022 Liu XZ, Rulina A, Choi MH, Pedersen L, Lepland J, Takle ST, Madeleine N, Peters SD, Wogsland CE, Grøndal SM, Lorens JB, Goodarzi H, Lønning PE, Knappskog S, Molven A, Halberg N
• A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy.
  Genome medicine 2021 Yogodzinski C, Arab A, Pritchard JR, Goodarzi H, Gilbert LA
• ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance.
  Cell 2021 Xu Y, Huangyang P, Wang Y, Xue L, Devericks E, Nguyen HG, Yu X, Oses-Prieto JA, Burlingame AL, Miglani S, Goodarzi H, Ruggero D
• Targeting KRAS4A splicing through the RBM39/DCAF15 pathway inhibits cancer stem cells.
  Nature communications 2021 Chen WC, To MD, Westcott PMK, Delrosario R, Kim IJ, Philips M, Tran Q, Bollam SR, Goodarzi H, Bayani N, Mirzoeva O, Balmain A
• Revealing molecular pathways for cancer cell fitness through a genetic screen of the cancer translatome.
  Cell reports 2021 Kuzuoglu-Ozturk D, Hu Z, Rama M, Devericks E, Weiss J, Chiang GG, Worland ST, Brenner SE, Goodarzi H, Gilbert LA, Ruggero D
• A Wnt twist in FTO's role in cancer progression.
  Nature cancer 2021 Navickas A, Goodarzi H
• OMIC-03. TRANSLATIONAL CONTROL IN MYC AND MYCN MEDULLOBLASTOMA.
  Neuro-Oncology 2021 Christin Schmidt, Albertas Navickas, Frederique Zindy, Dana Farmer, Davide Ruggero, Hani Goodarzi, Martine F Roussel, Bjoern Schwer, William Weiss
• A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements.
  Science (New York, N.Y.) 2021 Fish L, Khoroshkin M, Navickas A, Garcia K, Culbertson B, Hänisch B, Zhang S, Nguyen HCB, Soto LM, Dermit M, Mardakheh FK, Molina H, Alarcón C, Najafabadi HS, Goodarzi H
• Neuronal Nsun2 Deficiency is Associated With Codon-Specific Epitranscriptomic Dysregulation of Gly-Trnas and Corresponding Proteomic Shift Impacting Synaptic Signaling and Behavior.
  Biological Psychiatry 2021 Jennifer Blaze, Hannah Phillips, Soeren Heissel, Albertas Navickas, Amara Plaza-Jennings, Marcus Foo, Christopher Katanski, Christopher Watkins, Zachary Pennington, Behnam Javidfar, Sergio Espeso-Gil,…
• Abstract PS19-01: A sense-antisense RNA interaction drives metabolic reprogramming in metastatic breast cancer.
  Cancer Research 2021 Hani Goodarzi, Bruce Culbertson, Kristle Garcia, Lisa Fish
• A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression.
  The EMBO journal 2020 Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, Goodarzi H, Tavazoie SF
• Massively multiplex single-molecule oligonucleosome footprinting.
  eLife 2020 Abdulhay NJ, McNally CP, Hsieh LJ, Kasinathan S, Keith A, Estes LS, Karimzadeh M, Underwood JG, Goodarzi H, Narlikar GJ, Ramani V
• Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men.
  Cell stem cell 2020 Samuel RM, Majd H, Richter MN, Ghazizadeh Z, Zekavat SM, Navickas A, Ramirez JT, Asgharian H, Simoneau CR, Bonser LR, Koh KD, Garcia-Knight M, Tassetto M, Sunshine S, Farahvashi S, Kalantari A, Liu W,…
• Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells.
  Cell metabolism 2020 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, Goodarzi H, Birsoy K
• Tumoural activation of TLR3-SLIT2 axis in endothelium drives metastasis.
  Nature 2020 Tavora B, Mederer T, Wessel KJ, Ruffing S, Sadjadi M, Missmahl M, Ostendorf BN, Liu X, Kim JY, Olsen O, Welm AL, Goodarzi H, Tavazoie SF
• Artificial Intelligence for COVID-19 Drug Discovery and Vaccine Development.
  Frontiers in artificial intelligence 2020 Keshavarzi Arshadi A, Webb J, Salem M, Cruz E, Calad-Thomson S, Ghadirian N, Collins J, Diez-Cecilia E, Kelly B, Goodarzi H, Yuan JS
• The DNA methylation landscape of advanced prostate cancer.
  Nature genetics 2020 Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, …
• RBMS1 Suppresses Colon Cancer Metastasis through Targeted Stabilization of Its mRNA Regulon.
  Cancer discovery 2020 Yu J, Navickas A, Asgharian H, Culbertson B, Fish L, Garcia K, Olegario JP, Dermit M, Dodel M, Hänisch B, Luo Y, Weinberg EM, Dienstmann R, Warren RS, Mardakheh FK, Goodarzi H
• Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men.
  bioRxiv : the preprint server for biology 2020 Ghazizadeh Z, Majd H, Richter M, Samuel R, Zekavat SM, Asgharian H, Farahvashi S, Kalantari A, Ramirez J, Zhao H, Natarajan P, Goodarzi H, Fattahi F
• Abstract PD8-07: A pro-metastatic alternative splicing program that drives breast cancer progression.
  Cancer Research 2020 Hani Goodarzi, Lisa Fish, Bruce Culbertson
• The LC3-conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles.
  Nature cell biology 2020 Leidal AM, Huang HH, Marsh T, Solvik T, Zhang D, Ye J, Kai F, Goldsmith J, Liu JY, Huang YH, Monkkonen T, Vlahakis A, Huang EJ, Goodarzi H, Yu L, Wiita AP, Debnath J
• PCK1 and DHODH drive colorectal cancer liver metastatic colonization and hypoxic growth by promoting nucleotide synthesis.
  eLife 2019 Yamaguchi N, Weinberg EM, Nguyen A, Liberti MV, Goodarzi H, Janjigian YY, Paty PB, Saltz LB, Kingham TP, Loo JM, de Stanchina E, Tavazoie SF
• Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay.
  Molecular cell 2019 Fish L, Navickas A, Culbertson B, Xu Y, Nguyen HCB, Zhang S, Hochman M, Okimoto R, Dill BD, Molina H, Najafabadi HS, Alarcón C, Ruggero D, Goodarzi H
• A massively parallel 3' UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization.
  Genome research 2019 Litterman AJ, Kageyama R, Le Tonqueze O, Zhao W, Gagnon JD, Goodarzi H, Erle DJ, Ansel KM
• A regulatory program that promotes metastasis in colorectal cancer (CRC) through modulation of mRNA stability.
  Journal of Clinical Oncology 2019 Hani Goodarzi, Robert S. Warren, Johnny Yu, Lisa Fish
• FTO controls reversible m6Am RNA methylation during snRNA biogenesis.
  Nature chemical biology 2019 Mauer J, Sindelar M, Despic V, Guez T, Hawley BR, Vasseur JJ, Rentmeister A, Gross SS, Pellizzoni L, Debart F, Goodarzi H, Jaffrey SR
• Cancer cells exploit an orphan RNA to drive metastatic progression.
  Nature medicine 2018 Fish L, Zhang S, Yu JX, Culbertson B, Zhou AY, Goga A, Goodarzi H
• Publisher Correction: Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease.
  Nature communications 2018 Alkallas R, Fish L, Goodarzi H, Najafabadi HS
• Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
  Cell 2018 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, …
• Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
  Cell 2018 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, …
• Erratum: Asparagine bioavailability governs metastasis in a model of breast cancer.
  Nature 2018 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, …
• Asparagine bioavailability governs metastasis in a model of breast cancer.
  Nature 2018 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, …
• Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease.
  Nature communications 2017 Alkallas R, Fish L, Goodarzi H, Najafabadi HS
• Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface.
  PeerJ 2017 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
• Charting the "unknown unknowns" of cancer progression.
  Science translational medicine 2017 Goodarzi H
• MicroRNA-203 predicts human survival after resection of colorectal liver metastasis.
  Oncotarget 2017 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
• TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer.
  Cancer research 2016 Lee H, Goodarzi H, Tavazoie SF, Alarcón CR
• Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
  Cell 2016 Goodarzi H, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF
• Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness.
  Nature communications 2016 Nguyen A, Yoshida M, Goodarzi H, Tavazoie SF
• PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage.
  Cell reports 2016 Hwang HW, Park CY, Goodarzi H, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB
• Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts.
  Genes & development 2016 Fish L, Pencheva N, Goodarzi H, Tran H, Yoshida M, Tavazoie SF
• HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events.
  Cell 2015 Alarcón CR, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF
• Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival.
  Nature cell biology 2015 Furlow PW, Zhang S, Soong TD, Halberg N, Goodarzi H, Mangrum C, Wu YG, Elemento O, Tavazoie SF
• Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement.
  Cell 2015 Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF
• N6-methyladenosine marks primary microRNAs for processing.
  Nature 2015 Alarcón CR, Lee H, Goodarzi H, Halberg N, Tavazoie SF
• Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.
  Nature 2014 Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF
• Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts.
  Cell reports 2014 Oikonomou P, Goodarzi H, Tavazoie S
• TARBP2 binding structured RNA elements drives metastasis.
  Cell cycle (Georgetown, Tex.) 2014 Goodarzi H, Tavazoie SF, Tavazoie S
• Revealing the genetic basis of natural bacterial phenotypic divergence.
  Journal of bacteriology 2013 Freddolino PL, Goodarzi H, Tavazoie S
• A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model.
  Cell reports 2013 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
• Fitness landscape transformation through a single amino acid change in the rho terminator.
  PLoS genetics 2012 Freddolino PL, Goodarzi H, Tavazoie S
• Systematic discovery of structural elements governing stability of mammalian messenger RNAs.
  Nature 2012 Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S
• Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.
  Nature medicine 2011 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
• Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli.
  Molecular systems biology 2010 Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S
• Revealing global regulatory perturbations across human cancers.
  Molecular cell 2009 Goodarzi H, Elemento O, Tavazoie S
• Universal function-specificity of codon usage.
  Nucleic acids research 2009 Najafabadi HS, Goodarzi H, Salavati R
• Global discovery of adaptive mutations.
  Nature methods 2009 Goodarzi H, Hottes AK, Tavazoie S
• Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli.
  PLoS pathogens 2009 Amini S, Goodarzi H, Tavazoie S
• Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons.
  Gene 2007 Goodarzi H, Torabi N, Najafabadi HS, Archetti M
• Intragenic SNP haplotypes associated with 84dup18 mutation in TNFRSF11A in four FEO pedigrees suggest three independent origins for this mutation.
  Journal of bone and mineral metabolism 2007 Elahi E, Shafaghati Y, Asadi S, Absalan F, Goodarzi H, Gharaii N, Karimi-Nejad MH, Shahram F, Hughes AE
• Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix.
  Journal of theoretical biology 2006 Goodarzi H, Katanforoush A, Torabi N, Najafabadi HS
• The case for an error minimizing set of coding amino acids.
  Journal of theoretical biology 2006 Torabi N, Goodarzi H, Shateri Najafabadi H
• Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks.
  Computational biology and chemistry 2005 Marashi SA, Goodarzi H, Sadeghi M, Eslahchi C, Pezeshk H
• The impact of including tRNA content on the optimality of the genetic code.
  Bulletin of mathematical biology 2005 Goodarzi H, Najafabadi HS, Nejad HA, Torabi N
• On the coevolution of genes and genetic code.
  Gene 2005 Goodarzi H, Shateri Najafabadi H, Torabi N
• On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices.
  Journal of theoretical biology 2005 Goodarzi H, Najafabadi HS, Hassani K, Nejad HA, Torabi N
• Applying a neural network to predict the thermodynamic parameters for an expanded nearest-neighbor model.
  Journal of theoretical biology 2005 Najafabadi HS, Goodarzi H, Torabi N, Banihosseini SS
• Designing a neural network for the constraint optimization of the fitness functions devised based on the load minimization of the genetic code.
  Bio Systems 2005 Goodarzi H, Najafabadi HS, Torabi N
• Optimality of codon usage in Escherichia coli due to load minimization.
  Journal of theoretical biology 2005 Najafabadi HS, Goodarzi H, Torabi N
• Correspondence regarding Bharanidharan et al., "Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species".
  Biochemical and biophysical research communications 2004 Najafabadi HS, Goodarzi H
• On the optimality of the genetic code, with the consideration of termination codons.
  Bio Systems 2004 Goodarzi H, Nejad HA, Torabi N