Hani Goodarzi, PhD

Associate Professor
Biochemistry and Biophysics
+1 415 230-5189

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.

Publications: 

Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer.

Nature communications

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

The single-molecule accessibility landscape of newly replicated mammalian chromatin.

Cell

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

A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation.

Scientific reports

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

Author Correction: Systematic identification of post-transcriptional regulatory modules.

Nature communications

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

A Suite of Foundation Models Captures the Contextual Interplay Between Codons.

bioRxiv : the preprint server for biology

Naghipourfar M, Chen S, Howard M, Macdonald C, Saberi A, Hagen T, Mofrad M, Coyote-Maestas W, Goodarzi H

Functional screen for mediators of onco-mRNA translation specificity.

bioRxiv : the preprint server for biology

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

Tumor Cell Spatial Organization Directs EGFR/RAS/RAF Pathway Primary Therapy Resistance through YAP Signaling.

bioRxiv : the preprint server for biology

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

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 Perera, Davide Ruggero

Learning chemical sensitivity reveals mechanisms of cellular response.

Communications biology

Connell W, Garcia K, Goodarzi H, Keiser MJ

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.

Cell reports

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

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

pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease.

PLoS computational biology

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

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

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

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

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

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

Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman S

Effect of breast tissue density on cell-free orphan non-coding RNAs secreted by breast cancers.

Journal of Clinical Oncology

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, Pat Arensdorf, Lee S. Schwartzberg, Babak Alipanahi, Hani Goodarzi

Harnessing cell-free orphan non-coding RNAs as a predictive measure of long-term survival in neoadjuvant breast cancer therapy.

Journal of Clinical Oncology

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, Jennifer Yen, Irene Acerbi, Fereydoun Hormozdiari, Diane Heditsian, Laura Esserman, Laura van 't Veer, Hani Goodarzi, Babak Alipanahi

Stem-cell states converge in multistage cutaneous squamous cell carcinoma development.

Science (New York, N.Y.)

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

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

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

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, Pourmoghadam YK, Rotow JK, McCoach CE, Riess JW, Gutkind JS, Tang TT, Post L, Huang B, Santisteban P, Goodarzi H, Bandyopadhyay S, Kuo CJ, Roose JP, Wu W, Blakely CM, Roth JA, Bivona TG

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

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 Schwartzberg, Patrick Arensdorf, Hani Goodarzi, Fereydoun Hormozdiari, Babak Alipanahi

Abstract 1256: RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4.

Cancer research

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 Goodarzi, Franklin W. Huang

Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.

bioRxiv : the preprint server for biology

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

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

Chen S, Navickas A, Goodarzi H

Functional microRNA-targeting drug discovery by graph-based deep learning.

Patterns (New York, N.Y.)

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

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

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 J

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

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

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

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

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

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

Wang S, Böhnert V, Joseph AJ, Sudaryo V, Swinderman J, B Yu F, Lyu X, Skariah G, Subramanyam V, Gilbert LA, Goodarzi H, Li L

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.

bioRxiv : the preprint server for biology

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

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

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 Alipanahi

Detection of early-stage cancers using circulating orphan non-coding RNAs in blood.

Journal of Clinical Oncology

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, Hani Goodarzi, Lisa Fish, Fereydoun Hormozdiari, Babak Alipanahi

A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression.

Nature Cancer

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

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

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

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

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, Kocsis JD, Chen S, Studer L, Fattahi F

Abstract LB170: Artificial intelligence-assisted morphology-based detection and enrichment of malignant effusion tumor cells as a method for molecular profiling.

Cancer research

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, Chassidy Johnson, Amy L. Delson, Ron Balassanian, Jennifer Rosenbluth, Laura van't Veer, Michelle Melisko, Hope S. Rugo, Mahyar Salek, Maddison Masaeli, Hani Goodarzi

Abstract 5711: Blood-based early detection of non-small cell lung cancer using orphan noncoding RNAs.

Cancer research

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 Arensdorf, Kimberly H. Chau, Helen Li, Hani Goodarzi, Lisa Fish, Fereydoun Hormozdiari, Babak Alipanahi

Propagated Circulating Tumor Cells Uncover the Potential Role of NF?B, EMT, and TGF� Signaling Pathways and COP1 in Metastasis.

Cancers

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

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

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

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, Fereydoun Hormozdiari, Hani Goodarzi, Babak Alipanahi

SYF2 suppression mitigates neurodegeneration in models of diverse forms of ALS.

Cell stem cell

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, Goodarzi H, Ichida JK

Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance.

Molecular cancer

Stejskal P, Goodarzi H, Srovnal J, Hajd?ch M, van 't Veer LJ, Magbanua MJM

Functional microRNA-Targeting Drug Discovery by Graph-Based Deep Learning.

bioRxiv : the preprint server for biology

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

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

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

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

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

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

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

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

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, Laura Esserman, Laura van 't Veer

C/EBPB-dependent adaptation to palmitic acid promotes tumor formation in hormone receptor negative breast cancer.

Nature communications

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

Yogodzinski C, Arab A, Pritchard JR, Goodarzi H, Gilbert LA

ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance.

Cell

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

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

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

Navickas A, Goodarzi H

OMIC-03. TRANSLATIONAL CONTROL IN MYC AND MYCN MEDULLOBLASTOMA.

Neuro-oncology

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.)

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

Jennifer Blaze, Hannah Phillips, Soeren Heissel, Albertas Navickas, Amara Plaza-Jennings, Marcus Foo, Christopher Katanski, Christopher Watkins, Zachary Pennington, Behnam Javidfar, Sergio Espeso-Gil, Henrik Molina, Denise Cai, Tao Pan, Wei-Dong Yao, Hani Goodarzi, Fatemeh Haghighi, Schahram Akbarian

Abstract PS19-01: A sense-antisense RNA interaction drives metabolic reprogramming in metastatic breast cancer.

Cancer research

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

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

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

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, Andino R, Zhao H, Natarajan P, Erle DJ, Ott M, Goodarzi H, Fattahi F

Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells.

Cell metabolism

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

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

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

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, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY

RBMS1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon.

Cancer discovery

Yu J, Navickas A, Asgharian H, Culbertson B, Fish L, Garcia K, Olegario JP, Dermit M, Dodel M, Hanisch 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

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

The LC3-conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles.

Nature cell biology

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

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

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

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

Hani Goodarzi, Robert S. Warren, Johnny Yu, Lisa Fish

FTO controls reversible m6Am RNA methylation during snRNA biogenesis.

Nature chemical biology

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

Fish L, Zhang S, Yu JX, Culbertson B, Zhou AY, Goga A, Goodarzi H

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Cell

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

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

Erratum: Asparagine bioavailability governs metastasis in a model of breast cancer.

Nature

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

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

Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface.

PeerJ

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

Goodarzi H

MicroRNA-203 predicts human survival after resection of colorectal liver metastasis.

Oncotarget

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

Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.

Cell

Goodarzi H, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF

PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage.

Cell reports

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

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

Alarcón CR, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF

Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival.

Nature cell biology

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

Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF

N6-methyladenosine marks primary microRNAs for processing.

Nature

Alarcón CR, Lee H, Goodarzi H, Halberg N, Tavazoie SF

Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.

Nature

Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF

TARBP2 binding structured RNA elements drives metastasis.

Cell cycle (Georgetown, Tex.)

Goodarzi H, Tavazoie SF, Tavazoie S

Revealing the genetic basis of natural bacterial phenotypic divergence.

Journal of bacteriology

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

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

Systematic discovery of structural elements governing stability of mammalian messenger RNAs.

Nature

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

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

Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S

Revealing global regulatory perturbations across human cancers.

Molecular cell

Goodarzi H, Elemento O, Tavazoie S

Universal function-specificity of codon usage.

Nucleic acids research

Najafabadi HS, Goodarzi H, Salavati R

Global discovery of adaptive mutations.

Nature methods

Goodarzi H, Hottes AK, Tavazoie S

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

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

Goodarzi H, Katanforoush A, Torabi N, Najafabadi HS

The case for an error minimizing set of coding amino acids.

Journal of theoretical biology

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

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

Goodarzi H, Najafabadi HS, Nejad HA, Torabi N

On the coevolution of genes and genetic code.

Gene

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

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

Najafabadi HS, Goodarzi H, Torabi N, Banihosseini SS

Optimality of codon usage in Escherichia coli due to load minimization.

Journal of theoretical biology

Najafabadi HS, Goodarzi H, Torabi N

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