Albert Cheng

(*Equal contribution, # Co-correspondence)

1.    

Liu, Z., Jillette N., Robson, P., Cheng, A.W. (2023) Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold. Nucleic Acid Research gkad547 doi: 10.1093/nar/gkad547. IF=19.16

2.    

Buganim, Y., Lasry R., Maoz, N., Cheng, A.W., Tov, N.Y., Kulenkampff, E., Azagury, M., Yang, H., Ople, C., Markoulaki, S., Faddah D.A., Makedonski, K., Sabag, O., Jaenisch, R. (2023) Complex Haploinsufficiency in Pluripotent Cells Yields Somatic Cells with DNA Methylation Abnormalities and Pluripotency Induction Defects. Stem Cell Reports in press. IF=5.9

3.    

Clow, P.A., Du, M., Jillette, N., Taghbalout, A., Zhu, J.J.#, Cheng, A.W.# (2022) CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus. Nature Communications 13:1871. doi: 10.1038/s41467-022-29343-z. IF=17.694

4.    

Yi, E., Gujar, A.D., Guthrie, M., Kim, H., Zhao, D., Johnson K.C., Amin, S.B., Costa, M.L., Yu, Q., Das, S., Jillette, N., Clow, P.A., Cheng, A.W.#, Verhaak, R.G.W.# (2022) Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA hubs in cancer. Cancer Discovery doi: 10.1158/2159-8290.CD-21-1376 (co-corresponding) IF=39.397

5.    

Zhu, J.J., Cheng, A.W. (2022) JACKIE: Fast enumeration of genome-wide single- and multi-copy CRISPR target sites and their off-target numbers. The CRISPR Journal doi: 10.1089/crispr.2022.0042 IF=4.321

6.    

Jillette, N., Zhu, J.J.#, Cheng, A.W.# (2022) Local recruitment of DNA repair proteins enhances CRISPR-ssODN-HDR editing. BioRxiv (preprint). doi: 10.1101/2022.04.13.488255

7.    

Jillette, N., Zhu, J.J.#, Cheng, A.W.# (2022) Targeted directional kilobase sequence insertion by combining prime editing with recombinases or integrases. BioRxiv (preprint). doi: 10.1101/2022.05.25.493515

8.    

Taghbalout, A., Jillette, N., Cheng, A.W. (2021) TALE.Sense: A Versatile DNA Sensor Platform for Live Mammalian Cells. ACS Synthetic Biology doi: 10.1021/acssynbio.1c00212 IF=5.249

9.    

Du, M.*, Jillette, N.*, Zhu, J.J., Li, S., Cheng, A.W. (2020) CRISPR Artificial Splicing Factors. Nature Communications 11:2973. doi: 10.1038/s41467-020-16806-4 IF=17.694

10. 

Zhu, J.J., Jillette, N., Li X., Cheng, A.W.#, Lau C.C.# (2020) C11orf95-RELA Reprograms 3D Epigenome in Supratentorial Ependymoma. Acta Neuropathologica doi: 10.1007/s00401-020-02225-8 (co-corresponding) IF=21.534

11. 

Ashoor, H., Chen, X., Rosikiewicz, W., Wang, J., Cheng, A.W., Wang, P., Ruan, Y., Li, S. (2020) Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data. Nature Communications 11:1173. doi: 10.1038/s41467-020-14974-x IF=17.694

12. 

Leclair, N., Brugiolo, M., Urbanski, L., Lawson, S.C., Thakar, K., Yurieva, M., George J., Hinson, J.T., Cheng, A., Graveley, B.R., Anczukow, O. (2020) Poison exon splicing regulates a coordinated network of SR protein expression during differentiation and tumorigenesis. Molecular Cell 80(4):468-665.e9 doi: 10.1016/j.molcel.2020.10.019. IF=19.33

13. 

Taghbalout, A., Du, M., Jillette, N., Rosikiewicz, W. Rath, A., Heinen, C., Li, S., Cheng, A.W. (2019) Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways. Nature Communications 10:4296. doi:10.1038/s41467-019-12339-7 IF=17.694

14. 

Jillette, N*., Du, M.*, Zhu, J.J., Cardoz, P., Cheng, A.W. (2019) Split Selectable Markers. Nature Communications 10:4968. doi: 10.1038/s41467-019-12891-2 IF=17.694

15. 

Cheng, A.W.*#, Jillette, N.*, Lee, P., Plaskon, D., Fujiwara, Y., Wang, W., Taghbalout, A., Wang, H.# (2016) Casilio: a versatile CRISPR-Cas9-Pumilio hybrid for gene regulation and genomic labeling. Cell Research 26:254–257. doi: 10.1038/cr.2016.3 PMID:26768771 (co-corresponding) IF=46.3

16. 

Liu X., Zhang Y., Cheng C., Cheng, A.W., Zhang, X., Li N., Xia, C., Wei, X., Liu X., Wang, H. (2016) CRISPR-Cas9-mediated multiplex gene editing in CAR-T cells. Cell Research 27:154-157. doi:10.1038/cr.2016.142 PMID: 27910851 IF=46.3

17. 

Wiles, M.V., Qin, W., Cheng, A.W., Wang, H. (2015) CRISPR-Cas9-mediated genome editing and guide RNA design. Mammlian Genome DOI 10.1007/s00335-015-9565-z IF=2.078

18. 

Qin, W., Dion, S.L., Kutny, P.M., Zhang, Y., Cheng, A.W., Jillette, N.L., Malhotra, A., Geurts, A.M., Chen, Y.-G., Wang, H. (2015) Efficient CRISPR/Cas9-mediated genome editing in mice by zygote electroporation of nuclease. Genetics 115.176594 IF=4.402

19. 

Cheng, A.W.*, Shi, J.*, Wong, P.*, Luo, K.L., Trepman, P., Wang, E.T., Choi, H., Burge, C.B., Lodish, H.F. (2014) Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood doi: 10.1182/blood-2013-12-542209 PMID: 24869935 IF=25.48

20. 

Han, Y., Slivano, O.J., Christie, C.K., Cheng, A.W., Miano, J.M. (2014) CRISPR-Cas9 Genome Editing of a Single Regulatory Element Nearly Abolishes Target Gene Expression in Mice. Arterioscler Thromb Vasc Biol. pii: ATVBAHA.114.305017. PMID: 25538209 IF=10.51

21. 

Katz, Y., Li, F., Lambert, N.J., Sokol, E.S., Tam, W.L., Cheng, A.W., Airoldi, E.M., Lengner, C.J., Gupta, P.B., Yu, Z., Jaenisch, R., Burge, C.B. (2014) Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state. Elife doi: 10.7554/eLife.03915. PMID: 25380226

22. 

Wu, X., Scott, D.A., Kriz, A.J., Chiu, A.C., Hsu, P.D., Dadon, D.B., Cheng, A.W., Trevino, A.E., Konermann, S., Chen, S., Jaenisch, R., Zhang, F., Sharp, P.A. (2014) Genome-wide binding of CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. doi: 10.1038/nbt.2889 PMID: 24752079

23. 

Maetzel, D.*, Sarkar, S.*, Wang, H., Abi-Mosleh, L., Xu, P., Cheng, A.W., Gao, Q., Mitalipova, M., Jaenisch, R. (2014) Genetic and Chemical Correction of Cholesterol Accumulation and Impaired Autophagy in Hepatic and Neural Cells Derived from Niemann-Pick Type C Patient-Specific iPS Cells. Stem Cell Reports doi: 10.1016/j.stemcr.2014.03.014

24. 

Dawlaty, M.M., Breiling, A., Le, T. Barrasa M.I., Raddatz, G., Gao, Q., Powell, B.E., Cheng, A.W., Faull, K.F., Lyko, F., Jaenisch R. (2014) Loss of Tet enzymes compromises proper differentiation of embryonic stem cells. Dev. Cell. 29(1):102-11 PMID: 24735881

25. 

Cheng, A.W.*, Wang, H.*, Yang, H, Shi, L., Katz, Y., Theunissen, T.W., Rangarajan, S., Shivalila, C.S., Dadon, D.B., Jaenisch, R. (2013) Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Research 23(10):1163-71 PMID: 23979020 IF=46.3

26. 

Li, Y., Wang, H., Muffat, J., Cheng, A.W., Orlando, D.A., Loven, J., Kwok, S., Feldman, D.A., Bateup, H.S., Gao Q., Hockemeyer, D., Mitalipova, M., Lewis, C.A., Heiden, W.G.V., Sur, M., Young, R.A., Jaenisch, R. (2013) Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett Syndrome neurons.Cell Stem Cell 13(4):446-58 PMID: 24094325

27. 

Rudenko, A., Dawlaty, M.M., Seo, J., Cheng, A.W., Meng, J., Le, T., Faull, K.F., Jaenisch, R., Tsai, L.H. (2013) Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron 79(6):1109-22 PMID: 24050401

28. 

Yang, H.*, Wang, H.*, Shivalila, C.S.*, Cheng, A.W., Shi, L., Jaenisch, R. (2013). One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154(6):1370-9 PMID: 23992847

29. 

Faddah, D.A., Wang, H., Cheng, A.W., Katz, Y., Buganim, Y., Jaenisch, R (2013). Single-cell analysis reveals that expression of nanog is biallelic and equally variable as that of other pluripotency factors in mouse ESCs. Cell Stem Cell 13(1):23-9 PMID: 23827708

30. 

Wang, H.*, Hu, Y.C.*, Markoulaki, S., Welstead, C.G., Cheng, A.W., Shivalila, C.S., Pyntikova, T., Dadon, D.B., Voytas, D.F., Bogdanove, A.J., Page, D.C., Jaenisch, R (2013). TALEN-mediated editing of the mouse Y chromosome. Nat. Biotechnol. 31(6):530-2 PMID: 23666012

31. 

Wang, H.*, Yang, H.*, Shivalila, C.S.*, Dawlaty, M.M., Cheng, A.W., Zhang, F., Jaenisch, R (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153(4):910-8 PMID: 23643243

32. 

Lodato, M.A., Ng, C.W.*, Wamstad, J.A.*, Cheng, A.W., Thai, K.K., Faenkel, E., Jaenisch, R., Boyer, L.A. (2013) SOX2 Co-occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State. PLoS Genet. 9(2):e1003288 PMID: 23437007

33. 

Dawlaty, M.M., Breiling, A., Le, T., Raddatz, G., Barrasa, M.I., Cheng, A.W., Gao, Q., Powell, B.E., Li, Z., Xu, M., Faull, K.F., Lyko, F., Jaenisch R. (2013) Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible with Postnatal Development. Dev. Cell 24(3):310-23 PMID: 23352810

34. 

Buganim, Y.*, Faddah D.A.*, Cheng, A.W., Itskovich, E., Markoulaki, S., Gantz, K., Klemm S.L., van Oudenaarden A., Jaenisch, R. (2012) Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase. Cell 150(6):1209-22 PMID: 22980981

35. 

Buganim, Y., Itskovich, E., Hu, Y.-C., Cheng, A.W., Ganz, K., Sarkar, S., Fu, D.D., Welstead, G., Page, D.C., Jaenisch, R. (2012) Direct Reprogramming of Fibroblasts into Embryonic Sertoli-like Cells by Defined Factors. Cell Stem Cell 11(3):373-86 PMID: 22958931

36. 

Welstead, G.G., Creyghton, M.P., Bilodeau, S., Cheng, A.W., Markoulaki, S., Young, R.A., Jaenisch R. (2012) X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner. Proc. Natl. Acad. Sci. U.S.A. 109(32):13004-9 PMID: 22826230

37. 

Shapiro, I.M. *, Cheng, A.W. *, Flytzanis, N.C., Balsamo, M., Condeelis, J.S., Oktay, M.H., Burge, C.B., Gertler, F.B. (2011) An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 7(8):e1002218 PMID: 21876675 (co-first) IF=6.02

38. 

Kim, J., Su, S.C., Wang, H., Cheng, A.W., Cassady, J.P., Lodato, M.A., Lengner, C.J., Chung, C.Y., Dawlaty, M.M., Tsai, L.H., Jaenisch R. (2011) Functional integration of dopaminergic neurons directly converted from mouse fibroblasts. Cell Stem Cell 9(5):413-9 PMID: 22019014

39. 

Wong, P., Hattangadi, S.M., Cheng, A.W., Frampton, G.M., Young, R.A., Lodish, H.F. (2011) Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes. Blood 118(16):e128-38 PMID: 21860024

40. 

Dawlaty, M.M., Ganz, K., Powell, B.E., Hu, Y.C., Markoulaki, S., Cheng, A.W., Gao, Q., Kim, J., Choi, S.W., Page, D.C., Jaenisch, R. (2011) Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. Cell Stem Cell 5;9(2):166-75 PMID: 21816367

41. 

Soldner, F., Laganière, J., Cheng, A.W., Hockemeyer, D., Gao, Q., Alagappan, R., Khurana, V., Golbe, L.I., Myers, R.H., Lindquist, S., Zhang, L., Guschin, D., Fong, L.K., Vu, B.J., Meng, X., Urnov, F.D., Rebar, E.J., Gregory, P.D., Zhang, H.S., Jaenisch, R. (2011) Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell 146(2):318-31 PMID: 21757228

42. 

Creyghton, M.P.*, Cheng A.W.*, Welstead, G.G., Kooistra, T., Carey, B.W., Steine, E.J., Hanna, J., Lodato, M.A., Frampton, G.M., Sharp, P.A., Boyer, L.A., Young, R.A., Jaenisch, R. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. U.S.A. 107(50):21931-6 PMID: 21106759 (co-first) IF=12.78, citations (2010-2022): 3736

43. 

Lengner C.J., Erwin, J.A.*, Gimelbrant A.A.*, Cheng A.W., Guenther M.G., Welstead G.G., Alagappan R., Frampton M.F., Xu P., Powers D., Barrett C.B., Young R.A., Lee J.T., Jaenisch R., Mitalipova, M. (2010) Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 141(5):872-83 PMID: 20471072

44. 

Hanna J., Cheng, A.W., Saha K., Kim J.P., Lengner, C.J., Soldner, F., Cassady, J.P., Muffat, J., Carey, B.W., Jaenisch R. (2010) Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs. Proc. Natl. Acad. Sci. U.S.A.107(20):9222-7 PMID: 20442331

45. 

Hanna, J.*, Markoulaki, S.*, Mitalipova, M., Cheng, A.W., Cassady, J.P., Staerk, J., Carey, B.W., Lengner, C.J., Foreman, R., Love, J., Gao, Q., Kim, J., Jaenisch, R. (2009) Metastable Pluripotent States in NOD-Mouse-Derived ESCs. Cell Stem Cell 4(6):513-24 PMID: 19427283

46. 

Markoulaki, S.*, Hanna, J.*, Beard, C., Carey, B.W., Cheng, A.W., Lengner, C.J., Dausman, J.A., Fu, D., Gao, Q., Wu, S., Cassady, J.P. and Jaenisch, R. (2008) Transgenic mice with defined combinations of drug-inducible reprogramming factors. Nat Biotechnol 27(2):169-71 PMID: 19151700

47. 

Lo, K.Y., Chin, W. H., Ng, Y. P., Cheng, A. W., Cheung, Z. H and Ip, N. Y. (2005) SLAM-associated protein (SAP) as a potential negative regulator in Trk signaling. J Biol Chem 280(50):41744-52 PMID: 16223723