Publications
Zheng Y*, Caron D*, Kim J, Jun S, Tian Y, Florian M, Stuart K, Sims P, Gottardo R. . Nat Commun. 2025 Jul 1;16(1):5852. doi: 10.1038/s41467-025-61023-6. PMID: 40595741; PMCID: PMC12218154.
Zheng Y, Ahmad K, Henikoff S. . Proc Natl Acad Sci U S A. 2025 May 6;122(18):e2505385122. doi: 10.1073/pnas.2505385122. Epub 2025 May 2. PMID: 40314975; PMCID: PMC12067283.
Henikoff S*, Zheng Y*, Paranal R, Xu Y, Greene J, Henikoff J, Russell Z, Szulzewsky F, Thirimanne H, Kugel S, Holland E, Ahmad K. . Science. 2025 Jan 2;387(6735):737-743. doi: 10.1126/science.ads2169. Epub 2025 Feb 13. PMID: 39946483; PMCID: PMC12184985.
Fiorenza S*, Zheng Y*, Purushe J, Bock T, Sarthy J, Janssens D, Sheih A, Kimble E, Kirchmeier D, Phi T, Gauthier J, Hirayama A, Riddell S, Wu Q, Gottardo R, Maloney D, Yang J, Henikoff S, Turtle C. . Nat Commun. 2024 Sep 27;15(1):8309. doi: 10.1038/s41467-024-52503-2. PMID: 39333103; PMCID: PMC11436946.
Zheng Y*, Shen S*, Kele? S. . Genome Biol. 2022 Oct 17;23(1):222. doi: 10.1186/s13059-022-02774-z. PMID: 36253828; PMCID: PMC9575231.
Shen S, Zheng Y+, Kele? S. . Bioinformatics. 2022 Jul 11;38(14):3642-3644. doi: 10.1093/bioinformatics/btac372. PMID: 35652733; PMCID: PMC9272792.
Germanos AA, Arora S, Zheng Y, Goddard ET, Coleman IM, Ku AT, Wilkinson S, Amezquita RA, Zager M, Long A, Yang YC, Bielas J, Gottardo R, Ghajar C, Nelson P, Sowalsky A, Setty M, Hsieh A. . Elife. 2022 Dec 13;11:e79076. doi: 10.7554/eLife.79076. PMID: 36511483; PMCID: PMC9747158.
Cheng J, Clayton J, Acemel R, Zheng Y, Taylor R, Keles S, Harley J, Quail E, G¨®mez-Skarmeta J and Ulgiati D. . Front Immunol. 2022 Jun 13;13:901747. doi: 10.3389/fimmu.2022.901747. PMID: 35769482; PMCID: PMC9235356.
Zheng Y, Zhou P, Keles? S. . Methods. 2021 May;189:3-11. doi: 10.1016/j.ymeth.2020.07.001. Epub 2020 Jul 12. PMID: 32663510; PMCID: PMC7855360.
Huang K, Wu Y, Shin J, Zheng Y, Siahpirani A, Lin Y, Ni Z, Chen J, You J, Keles? S, Wang D, Roy S, Lu Q. . PLoS Genet. 2021 Feb 4;17(2):e1009309. doi: 10.1371/journal.pgen.1009309. PMID: 33539344; PMCID: PMC7888619.
Vitanza N, Biery M, Myers C, Ferguson E, Zheng Y, Girard E, Przystal J, Park G, Noll A, Pakiam F, Winter C, Morris S, Sarthy J, Cole B, Leary S, Crane C, Lieberman N, Mueller S, Nazarian J, Gottardo R, Brusniak M, Mhyre A, Olson J. . Neuro Oncol. 2021 Mar 25;23(3):376-386. doi: 10.1093/neuonc/noaa249. PMID: 33130903; PMCID: PMC7992886.
Wu S, Furlan S, Mihalas A, Kaya-Okur H, Feroze H, Emerson S, Zheng Y, Carson K, Cimino P, Keene C, Holland E, Sarthy J, Gottardo R, Ahmad K, Henikoff S, Patel A. . Nat Biotechnol. 2021 Jul;39(7):819-824. doi: 10.1038/s41587-021-00865-z. Epub 2021 Apr 12. PMID: 33846646; PMCID: PMC8277750.
Zheng Y, Keles? S. . Nat Methods. 2020 Jan;17(1):37-40. doi: 10.1038/s41592-019-0624-3. Epub 2019 Nov 11. PMID: 31712779; PMCID: PMC8136837.
Liao R*, Zheng Y*, Liu X, Zhang Y, Seim G, Tanimura N, Wilson G, Hematti P, Coon J, Fan J, Xu J, Keles? S+ and Bresnick E+. . Cell Rep. 2020 Jun 30;31(13):107832. doi: 10.1016/j.celrep.2020.107832. PMID: 32610133; PMCID: PMC7382780.
Zheng Y, Ahmad K, Henikoff K. . Protocols.io. (2020) dx.doi.org/10.17504/protocols.io.bjk2kkye. 52,354 views, 4,355 exports and 314 questions.
The ENCODE Project Consortium, et al. . Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. Erratum in: Nature. 2022 May;605(7909):E3. doi: 10.1038/s41586-021-04226-3. PMID: 32728249; PMCID: PMC7410828.
The ENCODE Project Consortium, et al. . Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. Erratum in: Nature. 2022 May;605(7909):E4. doi: 10.1038/s41586-021-04213-8. PMID: 32728248; PMCID: PMC7410827.
Zheng Y, Ay F, Keles? S. . Elife. 2019 Jan 31;8:e38070. doi: 10.7554/eLife.38070. PMID: 30702424; PMCID: PMC6450682.
Soukup AA, Zheng Y, Mehta C, Liu P, Hofmann I, Zhou Y, Zhang J, Choi K, Johnson KD, Keles S, Bresnick EH. . J Clin Invest. 2019 Mar 1;129(3):1180-1192. doi: 10.1172/JCI122694. Epub 2019 Feb 11. PMID: 30620726; PMCID: PMC6391105.
Tanimura N, Liao R, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang Y, Zheng Y, Keles? S, Xu J, Coon J, Bresnick E. . Dev Cell. 2018 Sep 10;46(5):581-594.e4. doi: 10.1016/j.devcel.2018.07.022. Epub 2018 Aug 16. PMID: 30122630; PMCID: PMC6133724.
Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keles? S. . PLoS Comput Biol. 2015 Oct 20;11(10):e1004491. doi: 10.1371/journal.pcbi.1004491. PMID: 26484757; PMCID: PMC4618727.