Albert Cheng

1.     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.# (2021) 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)

2.     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

3.     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

4.     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)

5.     Clow, P.A., Jillette, N., Zhu, J.J., Cheng, A.W. (2020) CRISPR-mediated Multiplexed Live Cell Imaging of Nonrepetitive Genomic Loci. BioRxiv (preprint) doi: 10.1101/2020.03.03.974923

6.     Zhu, J.J., Cheng, A.W. (2020) JACKIE: Fast enumeration of single- and multi-copy CRISPR binding sites. BioRxiv (preprint) doi: 10.1101/2020.02.27.968933

7.     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

8.     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.

9.     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

10.  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

11.  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)

12.  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

13.  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

14.  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

15.  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

16.  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

17.  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

18.  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

19.  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

20.  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

21.  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

22.  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

23.  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

24.  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

25.  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

26.  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

27.  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

28.  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

29.  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

30.  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

31.  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

32.  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

33.  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)

34.  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

35.  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

36.  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

37.  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

38.  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)

39.  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

40.  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

41.  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

42.  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

43.  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