Publications

Selected Publications

Preprints

• Machine learning analysis of population-wide plasma proteins identifies hormonal biomarkers of Parkinson’s Disease
  Fayzan Chaudhry, Tae Wan Kim, Olivier Elemento, Doron Betel
  medRxiv , December 2024
  [Preprint] [PubMed] [source code]
  
  
• A deep-learning tool for species-agnostic integration of cancer cell states
  Jonathan Rub, Jason E Chan, Carleigh Sussman, William D. Tap, Samuel Singer, Tuomas Tammela^*, Doron Betel^*
  bioRxiv , December 2024
  [Preprint] [PubMed] [source code]
  
  
• Multi-Omic Atlas reveals cytotoxic phenotype and ROS-linked metabolic quiescence as key features of CTL-resistant HIV-infected CD4+ T-cells
  Alberto Herrera, Louise Leyre, Jared Weiler, Noemi Luise Linden, Tan Thinh Huynh, Feng Wang, Colin Kovacs, Marina Caskey, Paul Zumbo, Maider Astorkia Amiama, Sandra Terry, Ya-Chi Ho, Doron Betel, R. Brad Jones
  bioRxiv , December 2024
  [Preprint] [PubMed]
  
  
• An IFN-STAT1-CYBB Axis Defines Protective Plasmacytoid DC to Neutrophil Crosstalk During Aspergillus fumigatus Infection
  Yahui Guo, Mariano A. Aufiero, Kathleen A.M. Mills, Simon A. Grassmann, Hyunu Kim, Paul Zumbo, Mergim Gjonbalaj, Audrey Billips, Katrina B. Mar, Yao Yu, Doron Betel, Joseph C. Sun, Tobias M. Hohl.
  bioRxiv , December 2024
  [Preprint] [PubMed] [source code]
  
  
• CAR-engineered lymphocyte persistence is governed by a FAS ligand/FAS auto-regulatory circuit.
  Yi F, Cohen T, Zimmerman N, Dündar F, Zumbo P, Eltilib R, Brophy EJ, Arkin H, Feucht J, Gormally MV, Hackett CS, Kropp KN, Etxeberria I, Chandran SS, Park JH, Hsu KC, Sadelain M, Betel D, Klebanoff CA.
  bioRxiv , 2024 March 31
  [Preprint] [PubMed] [source code]
  
  
• Identifying novel age-modulating compounds and quantifying cellular aging using novel computational framework for evaluating transcriptional age
  Zhang C, Saurat N, Cornacchia D, Chung SY, Sikder T, Minotti A, Studer L, Betel D.
  bioRxiv , 2023 October 4
  [Preprint] [PubMed]
  
  

2021 - Present

• Cross-species single-cell RNA-seq analysis reveals disparate and conserved cardiac and extracardiac inflammatory responses upon heart injury.
  Cortada E, Yao J, Xia Y, Dündar F, Zumbo P, Yang B, Rubio-Navarro A, Perder B, Qiu M, Pettinato AM, Homan EA, Stoll L, Betel D*, Cao J*, Lo JC*.
  Communication Biology , 2024 December 3
  [Publication] [PubMed] [source code]
  
  
• Selenocysteine tRNA methylation promotes oxidative stress resistance in melanoma metastasis.
  Nease LA, Church KP, Delclaux I, Murakami S, Astorkia M, Zerhouni M, Cascio G, Hughes RO, Aguirre KN, Zumbo P, Dow LE, Jaffrey S, Betel D, Piskounova E.
  Nature Cancer , 2024 December 5
  [Publication] [PubMed] [source code]
  
  
• A Classical Epithelial State Drives Acute Resistance to KRAS Inhibition in Pancreatic Cancer
  Singhal A, Styers HC, Rub J, Li Z, Torborg SR, Kim JY, Grbovic-Huezo O, Feng H, Tarcan ZC, Sahin Ozkan H, Hallin J, Basturk O, Yaeger R, Christensen JG, Betel D, Yan Y, Chio IIC, de Stanchina E, Tammela T.
  Cancer Discovery , 2024 November
  [Publication] [PubMed]
  
  
• Genome-wide CRISPR screen identifies neddylation as a regulator of neuronal aging and AD neurodegeneration
  Saurat N, Minotti AP, Rahman MT, Sikder T, Zhang C, Cornacchia D, Jungverdorben J, Ciceri G, Betel D, Studer L.
  Cell Stem Cell , 2024 August
  [Publication] [PubMed]
  
  
• Intratumoral immune triads are required for immunotherapy-mediated elimination of solid tumors
  Espinosa-Carrasco G, Chiu E, Scrivo A, Zumbo P, Dave A, Betel D, Kang SW, Jang HJ, Hellmann MD, Burt BM, Lee HS, Schietinger A.
  Cancer Cell , 2024 July 8
  [Publication] [PubMed] [source code]
  
  
• TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons
  Kim TW, Koo SY, Riessland M, Chaudhry F, Kolisnyk B, Cho HS, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L.
  Cell , 2024 June 11
  [Publication] [PubMed] [source code]
  
  
• Hallmarks of CD8+ T cell dysfunction are established within hours of tumor antigen encounter before cell division
  Rudloff MW, Zumbo P, Favret NR, Roetman JJ, Detrés Román CR, Erwin MM, Murray KA, Jonnakuti ST, Dündar F, Betel D, Philip M.
  Nature Immunology , 2023 Sept. 24(9)
  [Publication] [PubMed] [source code]
  
  
• A beta cell subset with enhanced insulin secretion and glucose metabolism is reduced in type 2 diabetes
  Rubio-Navarro A, Gómez-Banoy N, Stoll L, Dündar F, Mawla AM, Ma L, Cortada E, Zumbo P, Li A, Reiterer M, Montoya-Oviedo N, Homan EA, Imai N, Gilani A, Liu C, Naji A, Yang B, Chong ACN, Cohen DE, Chen S, Cao J, Pitt GS, Huising MO, Betel D, Lo JC.
  Nature Cell Biology , 2023 April 25(4)
  [Publication] [PubMed]
  
  
• Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration
  Xia Y, Duca S, Perder B, Dündar F, Zumbo P, Qiu M, Yao J, Cao Y, Harrison MRM, Zangi L, Betel D, Cao J.
  Nature Communications , 2022 Dec. 13; 13(1)
  [Publication] [PubMed]
  
  
• TCR signal strength defines distinct mechanisms of T cell dysfunction and cancer evasion
  Shakiba M, Zumbo P, Espinosa-Carrasco G, Menocal L, Dündar F, Carson SE, Bruno EM, Sanchez-Rivera FJ, Lowe SW, Camara S, Koche RP, Reuter VP, Socci ND, Whitlock B, Tamzalit F, Huse M, Hellmann MD, Wells DK, Defranoux NA, Betel D, Philip M, Schietinger A. .
  J Exp. Medicine , 2022 Feb. 7; 219(2)
  [Publication] [PubMed] [source code]
  
  
• An autoimmune stem-like CD8 T cell population drives type 1 diabetes
  Gearty SV, Dündar F, Zumbo P, Espinosa-Carrasco G, Shakiba M, Sanchez-Rivera FJ, Socci ND, Trivedi P, Lowe SW, Lauer P, Mohibullah N, Viale A, DiLorenzo TP, Betel D*, Schietinger A.* .
  Nature , 2021 Nov 30;
  [Publication] [PubMed] [source code]
  
  
• Inducible and reversible inhibition of miRNA-mediated gene repression in vivo
  La Rocca G, King B, Shui B, Li X, Zhang M, Akat KM, Ogrodowski P, Mastroleo C, Chen K, Cavalieri V, Ma Y, Anelli V, Betel D, Vidigal J, Tuschl T, Meister G, Thompson CB, Lindsten T, Haigis K, Ventura A.
  Elife , 2021 Aug 31;10:e70948.
  [Publication] [PubMed]
  
  
• Selective BCL-XL Antagonists Eliminate Infected Cells from a Primary-Cell Model of HIV Latency but Not from Ex Vivo Reservoirs
  Ren Y, Huang SH, Macedo AB, Ward AR, Alberto WDC, Klevorn T, Leyre L, Copertino DC, Mota TM, Chan D, Truong R, Rohwetter T, Zumbo P, Dündar F, Betel D, Kovacs C, Benko E, Bosque A, Jones RB.
  Journal of Virology, 2021 Jul 12;95(15):e0242520. Epub 2021 Jul 12.
  [Publication] [PubMed]
  
  
• Impact of Use of Antibiotics on Response to Immune Checkpoint Inhibitors and Tumor Microenvironment
  Khan U, Ho K, Hwang EK, Peña C, Brouwer J, Hoffman K, Betel D, Sonnenberg GF, Faltas B, Saxena A, Weisiger KE, Oh S, Hissong E, RoyChoudhury A, Shah MA.
  Am J Clin Oncol., 2021 Jun 1;44(6):247-253.
  [Publication] [PubMed]
  
  
• Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer's disease.
  Guttikonda SR, Sikkema L, Tchieu J, Saurat N, Walsh RM, Harschnitz O, Ciceri G, Sneeboer M, Mazutis L, Setty M, Zumbo P, Betel D, de Witte LD, Pe'er D, Studer L.
  Nature Neurosci., 2021 Mar;24(3):343-354.
  [Publication] [PubMed]
  
  

2016 - 2020

• Multicenter Phase II Study of Cabazitaxel in Advanced Gastroesophageal Cancer: Association of HER2 Expression and M2-Like Tumor-Associated Macrophages with Patient Outcome.
  Shah MA, Enzinger P, Ko AH, Ocean AJ, Philip PA, Thakkar PV, Cleveland K, Lu Y, Kortmansky J, Christos PJ, Zhang C, Kaur N, Elmonshed D, Galletti G, Sarkar S, Bhinder B, Pittman ME, Plotnikova OM, Kotlov N, Frenkel F, Bagaev A, Elemento O, Betel D, Giannakakou P, Lenz HJ.
  Clinical Cancer Res.,2020 Sep 15;26(18):4756-4766. Epub 2020 Jul 8.
  [Publication] [PubMed]
  
  
• A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes.
  Cederquist GY, Tchieu J, Callahan SJ, Ramnarine K, Ryan S, Zhang C, Rittenhouse C, Zeltner N, Chung SY, Zhou T, Chen S, Betel D, White RM, Tomishima M, Studer L.
  Cell Stem Cell, 2020 Jul 2;27(1):35-49.e6.
  [Publication] [PubMed]
  
  
• High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down.
  Li X, Pritykin Y, Concepcion CP, Lu Y, La Rocca G, Zhang M, King B, Cook PJ, Au YW, Popow O, Paulo JA, Otis HG, Mastroleo C, Ogrodowski P, Schreiner R, Haigis KM, Betel D, Leslie CS, Ventura A.
  Mol Cell, 2020 Jul 2;79(1):167-179.e11. Epub 2020 Jun 3.
  [Publication] [PubMed]
  
  
• TOX is a critical regulator of tumour-specific T cell differentiation.
  Scott AC, Dündar F, Zumbo P, Chandran SS, Klebanoff CA, Shakiba M, Trivedi P, Menocal L, Appleby H, Camara S, Zamarin D, Walther T, Snyder A, Femia MR, Comen EA, Wen HY, Hellmann MD, Anandasabapathy N, Liu Y, Altorki NK, Lauer P, Levy O, Glickman MS, Kaye J, Betel D, Philip M, Schietinger A.
  Nature , 2019 Jul;571(7764):270-274. doi: . Epub 2019 Jun 17.
  [Publication] [PubMed]
  
  
• Lipid Deprivation Induces a Stable, Naive-to-Primed Intermediate State of Pluripotency in Human PSCs
  Cornacchia D, Zhang C, Zimmer B, Chung SY, Fan Y, Soliman MA, Tchieu J, Chambers SM, Shah H, Paull D, Konrad C, Vincendeau M, Noggle SA, Manfredi G,Finley LWS, Cross JR, Betel D, Studer L
  Cell Stem Cell , 2019 May 21. pii: S1934-5909(19)30205-X
  [Publication] [PubMed]
  
  
• Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation
  Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D
  Nature Genetics , 2019 Jun;51(6):999-1010
  [Publication] [PubMed]
  
  
• A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples
  Zhang C, Thakkar PV, Powell SE, Sharma P, Vennelaganti S, Betel D, Shah MA
  Front Microbiol. , 2019 Jan 8;9:3246
  [Publication] [PubMed]
  
  
• Extracellular vesicles in DLBCL provide abundant clues to aberrant transcriptional programming and genomic alterations
  Rutherford SC, Fachel AA, Li S, Sawh S, Muley A, Ishii J, Saxena A, Dominguez PM, Caldas Lopes E, Agirre X, Chambwe N, Correa F, Jiang Y, Richards KL, Betel D*, Shaknovich R*
  Blood , 2018 Aug 16;132(7):e13-e23
  [Publication] [PubMed]
  
  
• "Same difference": comprehensive evaluation of four DNA methylation measurement platforms
  Kacmarczyk TJ, Fall MP, Zhang X, Xin Y, Li Y, Alonso A, Betel D
  Epigenetics Chromatin , 2018 May 25;11(1):21.
  [Publication] [PubMed] [source code]
  
  
• Unifying cancer and normal RNA sequencing data from different sources
  Wang Q, Armenia J, Zhang C, Penson AV, Reznik E, Zhang L, Minet T, Ochoa A, Gross BE, Iacobuzio-Donahue CA, Betel D, Taylor BS, Gao J, Schultz N
  Sci Data. , 2018 Apr 17;5:180061.
  [Publication] [PubMed]
  
  
• Early-onset Colorectal Cancer is Distinct From Traditional Colorectal Cancer
  Yeo H, Betel D, Abelson JS, Zheng XE, Yantiss R, Shah MA.
  Clinical Colorectal Cancer , 2017 Dec;16(4):293-299.e6
  [Publication] [PubMed] [source code & data]
  
  
• CryoPause: A New Method to Immediately Initiate Experiments after Cryopreservation of Pluripotent Stem Cells
  Wong KG, Ryan SD, Ramnarine K, Rosen SA, Mann SE, Kulick A, De Stanchina E, Müller FJ, Kacmarczyk TJ, Zhang C, Betel D, Tomishima MJ.
  Stem Cell Reports , 2017 Jul 11;9(1):355-365
  [Publication] [PubMed]
  
  
• The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research
  Zhang C, Powell SE, Betel D, Shah MA.
  Hematol Oncol Clin North Am., 2017 Jun;31(3):389-408
  [Publication] [PubMed]
  
  
• Encoding of contextual fear memory requires de novo proteins in the prelimbic cortex
  Rizzo V, Touzani K, Raveendra BL, Swarnkar S, Lora J, Kadakkuzha BM, Liu XA, Zhang C, Betel D, Stackman RW, Puthanveettil SV.
  Biol Psychiatry Cogn Neurosci Neuroimaging , 2017 Mar;2(2):158-169
  [Publication] [PubMed]
  
  

2011 - 2016

• Circulating Plasma Levels of MicroRNA-21 and MicroRNA-221 Are Potential Diagnostic Markers for Primary Intrahepatic Cholangiocarcinoma
  Correa-Gallego C, Maddalo D, Doussot A, Kemeny N, Kingham TP, Allen PJ, D'Angelica MI, DeMatteo RP, Betel D , Klimstra D, Jarnagin WR, Ventura A.
  PLoS One , 2016, Sep 29;11(9): e0163699
  [Publication] [PubMed]
  
  
• Identification of Low Abundance Microbiome in Clinical Samples Using Whole Genome Sequencing
  Zhang C., Cleveland K., Schnoll-Sussman F., McClure B., Bigg M., Thakkar P., Schultz N., Shah MA.*, Betel D*
  Genome Biology , 2015, 16:265,
  [Publication] [PubMed] [source code & data]
  
  
• Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection
  Kacmarczyk TJ, Bourque C, Zhang X, Jiang Y, Houvras Y, Alonso A, Betel D
  PLoS One ,2015 Jun 11;10(6),
  [Publication] [PubMed]
  
  
• An allelic series of miR-17∼92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron
  Han YC, Vidigal JA, Mu P, Yao E, Singh I, González AJ, Concepcion CP, Bonetti C, Ogrodowski P, Carver B, Selleri L, Betel D*, Leslie C*, Ventura A
  Nature Genetics ,2015 Jul;47(7):766-75,
  [Publication] [PubMed]
  
  
• Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution
  Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ , Ishii J, Betel D,, Alonso A, Mason CE, Figueroa ME, Melnick AM.
  JoVE , 2015 Feb 24;(96):e52246,
  [Publication] [PubMed]
  
  
• Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
  Rapaport F., Khanin R., Liang Y., Pirun M., Krek A., Zumbo P., Mason CE., Socci ND., Betel D.
  Genome Biology , 2013 Sep 10;14(9):R95, Highly Accessed
  [Publication] [PubMed] [arXiv] [source code & data]
  
  
• Genome-wide identification of miRNA targets by PAR-CLIP
  Hafner M, Lianoglou S, Tuschl T, Betel D.
  METHODS , 2012 Aug.19.
  [Publication] [PubMed] [data]
  
  
• The expanding role of miR-302-367 in pluripotency and reprogramming
  Lipchina I, Studer L, Betel D.
  Cell Cycle, 2012 Apr 15;11(8):1517-23
  [Publication] [PubMed]
  
  
• Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutants
  Sun K, Westholm JO, Tsurudome K, Hagen JW, Lu Y, Kohwi M, Betel D, Gao FB, Haghighi AP, Doe CQ, Lai EC.,
  PLoS Genet., 2012 Feb;8(2):e1002515
  [Publication] [PubMed]
  
  
• Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response
  Lipchina I, Elkabetz Y, Hafner M, Sheridan R, Mihailovic A,Tuschl T, Sander C, Studer L, Betel D
  Genes & Dev., 2011; 25:2173-2186
  [Publication] [PubMed]
  
  
• Widespread regulatory activity of vertebrate microRNA* species
  Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC,
  RNA, 2011 Feb;17(2):312-26
  [Publication] [PubMed]
  
  

2005-2010

• Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
  Betel D, Koppal A, Agius P, Sander C, Leslie CS
  Genome Biology, 2010;11(8):R90, Highly Accessed
  [Publication] [PubMed]
  
  
• Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B cell lymphomas
  Mu P, Han Y-C, Betel D, Yao E, Squatrito M, Ogrodowski P, Stanchina Ed, D’Andrea A, Sander C, Ventura A,
  Genes & Dev., 2009 Dec. 15,23:2806-11
  [Publication] [PubMed] [data]
  
  
• Characterization of small RNAs in aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB
  Rajasethupathy P, Fiumara F, Sheridan R, Betel D, Puthanveettil SV, Russo JJ, Sander C, Tuschl T, Kandel E,
  Neuron. 2009 Sep 24;63(6):803-17.
  [Publication] [PubMed]
  
  
• Transfection of small RNAs globally perturbs regulation by endogenous microRNAs
  Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS,
  Nature Biotechnology. 2009 Jun;27(6):549-55
  [Publication] [PubMed]
  
  
• The microRNA.org resource: targets and expression
  Betel D, Wilson M, Gabow A, Marks DS, Sander C.,
  Nucleic Acids Res. 2008 Jan;36(Database issue):D149-53.
  [Publication] PubMed
  
  
• Computational analysis of mouse piRNA sequence and biogenesis
  Betel D, Sheridan R, Marks DS, Sander C.,
  PLoS Comput Biol. 2007 Nov; 3(11):e222.
  [Publication] [PubMed]
  
  
• Structure-templated predictions of novel protein interactions from sequence information
  Betel D, Breitkreuz KE, Isserlin R, Dewar-Darch D, Tyers M, Hogue CW.
  PLoS Comput Biol. 2007 Sep 21;3(9):1783-9.
  [Publication] [PubMed]
  
  

2002 - 2005

• The Biomolecular Interaction Network Database and related tools 2005 update
  Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, ... , Pawson T, Ouellette BF, Hogue CW.,
  Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24.
  [Publication] [PubMed]
  
  
• Analysis of domain correlations in Yeast protein complexes
  Betel D, Isserlin R, Hogue CWV
  Bioinformatics 2004 Aug 4;20 Suppl1:i55-i62. (Proceedings of the 12th Int. Conference On Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference on Computational Biology, 2004.)
  [Publication] [PubMed]
  
  
• BIND - The Biomolecular Interaction Database
  Bader GD, Betel D, Hogue CWV,
  Nucleic Acids Res. 2003 Jan 1;31(1): 248-250.
  [Publication] [PubMed]
  
  
• SeqHound: biological sequence and structure database as a platform for bioinformatics research
  Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CWV
  BMC Bioinformatics 2002 Oct 25;3(1):32.
  [Publication] [PubMed]
  
  
• Mutation profiling of mismatch repair-deficient colorectal cancers using an in silico genome scan to identify coding microsatellites
  Park J*, Betel D*, Gryfe R, Michalickova K, Di Nicola N, Gallinger S, Hogue CWV, Redston M
  Cancer Res. 2002 Mar 1;62(5):1284-8.
  [Publication] [PubMed]
  
  

Book Chapter

• Systems Biology of microRNAs
  Betel D, Khanin R
  Handbook of Statistical Systems Biology, Eds. Stumpf M., Balding DJ., Girolami M., John Wiley & Sons, Dec. 2011, ISBN: 978-0-470-71086-9
  Wiley Online Library