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Ziyang Zhang , Madeline E. Melzer, Keerthana M. Arun, Hanxiao Sun, Carl-Johan Eriksson, Itai Fabian, Sagi Shaashua, Karun Kiani, Yaara Oren, Yogesh Goyal. Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms. Cell Genomics.2024.​

https://doi.org/10.1016/j.xgen.2024.100592

 

Kathrin Böpple, Yaara Oren, Whitney S. Henry, Meng Dong , Sandra Weller, Julia Thiel, Markus Kleih, Andrea Gaißler,Damaris Zipperer, Hans-Georg Kopp, Yael Aylon, Moshe Oren, Frank Essmann, Chunguang Liang  and Walter E. Aulitzky.  ATF3 characterizes aggressive drug-tolerant persister cells in HGSOC. Cell Death and Disease. 2024

https://doi.org/10.1038/s41419-024-06674-x

Noronha A, Belugali Nataraj N, Lee JS, Zhitomirsky B, Oren Y, Oster S, Lindzen M, Mukherjee S, Will R, Ghosh S, Simoni-Nieves A, Verma A, Chatterjee R, Borgoni S, Robinson W, Sinha S, Brandis A, Kerr DL, Wu W, Sekar A, Giri S, Chung Y, Drago-Garcia D, Danysh BP, Lauriola M, Fiorentino M, Ardizzoni A, Oren M, Blakely CM, Ezike J, Wiemann S, Parida L, Bivona TG, Aqeilan RI, Brugge JS, Regev A, Getz G, Ruppin E, Yarden Y.AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer.Cancer Discov. 2022 

https://aacrjournals.org/cancerdiscovery/article/12/11/2666/710003/AXL-and-Error-Prone-DNA-Replication-Confer-Drug

Oren Y. Standing on the shoulders of microbes: How cancer biologists are expanding their view of hard-to-kill persister cells. Mol Syst Biol. 2022.
https://www.embopress.org/doi/full/10.15252/msb.202211168


Oren Y. Hunting down rare drug-tolerant cycling cells with Watermelon. Nat Rev Cancer. 2022.
https://www.nature.com/articles/s41568-022-00483-0

Yaara Oren, Michael Tsabar, Michael S Cuoco, Liat Amir-Zilberstein, Heidie F. Cabanos, Jan-Christian Hütter, Bomiao Hu, , Pratiksha I. Thakore,  Marcin Tabaka, Charles P Fulco, William Colgan, Brandon M Cuevas, Sara A. Hurvitz, Dennis J. Slamon, Amy Deik, Kerry A Pierce, Clary Clish, Aaron Hata, Elma Zaganjor, Galit Lahav, Katerina Politi , Joan S. Brugge, Aviv Regev. Cycling cancer persister cells arise from lineages with distinct transcriptional and metabolic programs .Cycling cancer persister cells arise from lineages with distinct programs. 
Nature, 2021, 596(7873):576-582.
https://www.nature.com/articles/s41586-021-03796-6

Li CM, Shapiro H, Tsiobikas C, Selfors LM, Chen H, Rosenbluth J, Moore K, Gupta KP, Gray GK, Oren Y, Steinbaugh MJ, Guerriero JL, Pinello L, Regev A, Brugge JS.
Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing.
https://doi.org/10.1016/j.celrep.2020.108566

Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus, Li LH, Pelka K, Ge W, Oren Y, Brack A, Law T, Rodman C, Chen JH, Boland GM, Hacohen N, Rozenblatt-Rosen O, Aryee MJ, Buenrostro JD, Regev A, Sankaran VG.
Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.
Cell, 2019 7;176(6):1325-1339.e22.
https://doi.org/10.1016/j.cell.2019.01.022

Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR. Genetic and transcriptional evolution alters cancer cell line drug response.
Nature, 2018 560(7718):325-330.
https://doi.org/10.1038/s41586-018-0409-3

McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO, Corander J.
Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.
PLOS Genetics, 2018 12;12(9): e1006280.
https://doi.org/10.1371/journal.pgen.1006280

Huja S, Oren Y, Trost E, Brzuszkiewicz E, Biran D, Blom J, Goesmann A, Gottschalk G, Hacker J, Ron EZ, Dobrindt U.
Genomic avenue to avian colisepticemia.
MBio, 2015 13;6(1): e01681-14.
https://doi.org/10.1128/mbio.01681-14

Oren Y, Smith MB, Johns NI, Kaplan Zeevi M, Biran D, Ron EZ, Corander J, Wang HH, Alm EJ, Pupko T.
Transfer of noncoding DNA drives regulatory rewiring in bacteria.
Proceedings of the National Academy of Sciences, 2014 11;111(45):16112-16117.
https://doi.org/10.1073/pnas.1413272111

Huja S, Oren Y, Biran D, Meyer S, Dobrindt U, Bernhard J, Becher D, Hecker M, Sorek R, Ron EZ (2014).
Fur Is the Master Regulator of the
Extraintestinal Pathogenic Escherichia coli Response to Serum.
MBio, 2014 12;5(4): e01460-14.
https://doi.org/10.1128/mBio.01460-14

Rubinstein ND, Zeevi D, Oren Y, Segal G, Pupko T, The operonic location of auto-transcriptional repressors is highly conserved in bacteria (2011). Molecular Biology and Evolution, 28(12):3309-18.
https://doi.org/10.1093/molbev/msr163



 

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