a. peer-reviewed research articles (@ corresponding authors and * co-first authors from our lab):

2020-2025:

44.   Gandin, V.*, Kim, J.*, Yang, L., Lian, Y., Kawase, T., Hu, A., Rokicki, K., Fleishman, G., Tillberg, P., Castrejon, A.A., Stringer, C., Preibisch, S. Liu, Z.@ (2025) Deep-tissue transcriptomics and subcellular imaging at high spatial resolution. Science. DOI: doi.org/10.1126/science.adq2084; PMID: 39977545

43.   Dong, P.@, Zhang, S., Gandin, V., Xie, L., Wang, L., Lemire, A.L., Li, W., Otsuna, H., Kawase, T., Lander, A.D., Chang. H.Y., Liu, Z.@ (2024) Cohesin prevents cross-domain gene co-activation. Nature Genetics, 56(8):1654-1664. DOI: doi.org/10.1038/s41588-024-01852-1; PMID: 39048795

42.  Wong, V.C., Houlihan, P.R., Liu, H., Walpita, D., DeSantis, M.C., Liu, Z., O'Shea, E.K. (2024) Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking. Elife, 15;13:e80622. DOI: doi.org/10.7554/eLife.80622; PMID: 39146380

41.   Yang, L., Min, Y., Liu, Y., Gao, B., Liu, X., Huang, Y., Wang, H., Yang, L., Liu, Z., Chen, L. CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells. (2024) Nature Methods, 21(9):1646-1657. DOI: 10.1038/s41592-024-02333-3; PMID: 38965442

40.   Hao, S., Ye J.L., Goldfajn, N.B., Flores, E., Liang, J., Fuehrer, H., Demmerte, J., Lippincott-Schwartz, J., Liu, Z., Sukenik, S., Cai, D. (2024) YAP condensates are highly organized hubs. iScience, 27(6):109927. DOI: 10.1016/j.isci.2024.109927; PMID: 38784009

39.   Daugird, T.A., Shi, Y., Holland, K.L., Rostamian, H., Liu, Z., Lavis, L.D., Rodriguez, J., Strahl, B.D., Legant, W.R. (2024) Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nat. Commun., 15(1):4178 DOI: 10.1038/s41467-024-48562-0; PMID: 3875520

38.   Grimm, J.B., Tkachuk, A.N., Patel, R., Hennigan, S.T., Gutu, A., Dong, P., Gandin, V., Osowski, A.M., Holland, K.L., Liu, Z., Brown, T.A., Lavis, L.D. (2023) Optimized Red-Absorbing Dyes for Imaging and Sensing. JACS, 145(42):23000-23013. DOI: 10.1021/jacs.3c05273; PMID: 37842926

37.   Liu, Y., Huang, Z., Liu, H., Ji, Z., Arora, A., Cai, D., Wang, H., Liu, M., Simko, E.A., Zhang, Y., Periz, G., Liu, Z., Wang, J. (2023) DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat. Neuron, 111(8):1205-21. DOI: 10.1016/j.neuron.2023.01.022; PMID: 36822200

36.   Bonello, T.T., Cai D., Fletcher, G.C., Wiengartner, K., Pengilly, V., Lange, K.S., Liu, Z., Lippincott-Schwartz, J., Kavran, J.M., Thompson, B.J. (2023) Phase separation of Hippo signalling complexes. EMBO Journal, 42(6):e112863. DOI: 10.15252/embj.2022112863; PMID: 36807601

35.   Lange, J.T., Rose, J.C., Chen, C.Y., Pichugin, Y., Xie, L., Tang, J., Hung, K.L., Yost, K.E., Shi, Q., Erb, M.L., Rajkumar, U., Wu, S., Taschner-Mandl, S., Bernkopf, M., Swanton, C., Liu, Z., Huang, W., Chang, H.Y., Bafna, V., Henssen, A.G., Werner, B., Mischel, P.S. (2022) The evolutionary dynamics of extrachromosomal DNA in human cancers. Nature Genetics, 54(10):1527-1533. DOI: 10.1038/s41588-022-01177-x; PMID: 36123406

34.   Liu, H., Wang, P.G., Pitt, G., Liu, Z.@ (2022) Direct Observation of Compartment-Specific Localization and Dynamics of Voltage-Gated Sodium Channels. Journal of Neuroscience, 42(28):5482-5498. (Cover story) DOI: 10.1523/JNEUROSCI.0086-22.2022; PMID: 35672149

33.   Xie, L.*, Dong, P.*, Qi, Y., Hsieh, T.S., English, B., Jung, S., Chen, X., Marzio, M.D., Chen, X., Casellas, R., Chang, H.Y., Zhang, B.@, Tjian, R.@, Liu, Z.@ (2022) BRD2 Compartmentalizes the Accessible Genome. Nature Genetics, 54(4):481-491. DOI: 10.1038/s41588-022-01044-9; PMID: 35410381

32.  Hung, K.L.*, Yost, K.E.*, Xie, L.*, Shi, Q., Helmsauer, K., Luebeck, J., Schöpflin, R., Lange, J.T., Chamorro González, R., Weiser, N.E., Chen, C., Valieva, M.E., Wong, I.T., Wu, S., Dehkordi, S.R., Duffy, C.V., Kraft, K., Tang, J., Belk, J.A., Rose, J.C., Corces, M.R., Granja, J.M., Li, R., Rajkumar, U., Friedlein, J., Bagchi, A., Satpathy, A.T., Tjian, R., Mundlos, S., Bafna, V., Henssen, A.G., Mischel, P.S., Liu, Z., Chang, H.Y. (2021) ecDNA hubs drive cooperative intermolecular oncogene expression.  Nature, 600(7890):731-736. DOI: 10.1038/s41586-021-04116-8; PMID: 34819668

31.  Lerner, J., Gomez-Garcia, P.A., McCharhy, R.L., Liu, Z., Lakadamyali, M., Zaret, K.S. (2020). Two-parameter single-molecule analysis for measurement of chromatin mobility. STAR Protocols, 1(3):100223. DOI: 10.1016/j.xpro.2020.100223; PMID: 33377115

30.   Binns, T.C., Ayala, A.X., Grimm, J.B., Tkachuk, A.N., Castillon, G.A., Phan, S., Zhang, L., Brown, T.A., Liu, Z., Adams, S.R., Ellisman, M.H., Koyama, M., Lavis, L.D. (2020). Rational design of bioavailable photosensitizers for manipulation and imaging of biological systems. Cell Chemical Biology, 27(8):1063-72. DOI: 10.1016/j.chembiol.2020.07.001; PMID: 32698018

29.  Lerner, J., Gomez-Garcia, P.A., McCharhy, R.L., Liu, Z., Lakadamyali, M., Zaret, K.S. (2020). Two-parameter mobility assessments discriminate diverse regulatory factor behaviors in chromatin. Molecular Cell, 79(4):677-688. DOI: 10.1016/j.molcel.2020.05.036; PMID: 32574554

28.  Grimm, J.B., Tkachuk, A.N., Xie, L., Choi, H., Mohar, B., Falco, N., Schaefer, K., Patel, R., Zheng, Q., Liu, Z., Lippincott-Schwartz, J., Brown, T.A., Lavis, L.D. (2020). A general method to optimize and functionalize red-shifted rhodamine dyes. Nature Methods, 17(8):815-821 DOI: 10.1038/s41592-020-0909-6; PMID: 32719532

27.  Matthies, D., Lee, N.Y., Gatera, I., Pasolli, H.A., Zhao, X., Liu, H., Walpita, D., Liu, Z., Yu, Z., Ioannou, M.S. (2020). Microdomains form on the luminal face of neuronal extracellular vesicle membranes. Scientific Reports, 10(1):11953. DOI: 10.1038/s41598-020-68436-x; PMID: 32686698

26.   Ochiai, H., Hayashi, T., Umeda, M., Yoshimura, M., Harada, A., Shimizu, Y., Nakano, K., Saitoh, N., Kimura, H., Liu, Z., Yamamoto, T., Okamura, T., Ohkawa, Y., Kimura, H., Nikaido, I. (2020). Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. Science Advances, 17;6(25). DOI: 10.1126/sciadv.aaz6699; PMID: 32596448

25.  Xie, L.*, Dong, P.*, Qi, Y., Marzio, M.D., Chen, X., Banala, S., Legant, W.R., English, B., Hansen, A., Schulmann, A., Lavis, L.D., Betzig, E., Chang, H.Y., Zhang, B., Tjian, R.@, Liu, Z.@ (2020). 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature Methods, 17(4):430-436. DOI: 10.1038/s41592-020-0775-2; PMID: 32203384

2014-2019:

24.  Piccolo, F.M., Liu, Z., Deng, D., Hsu, C., Stoyanova, E.I., Rao, A., Tjian, R., Neintz, N. (2019). MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions. eLife, 8:e51449. DOI: 10.7554/eLife.51449; PMID: 31868585

23.  Ioannou M.S.*, Liu, Z., Lippincott-Schwartz, J. (2019). A neuron-glia co-culture system for studying intercellular lipid transport. Curr. Protoc. Cell Biol., 84(1): e95. DOI: 10.1002/cpcb.95; PMID: 31483110

22.  Cai, D., Feliciano, D., Dong, P., Flores, E., Gruebele, M., Porat-Shliom, N., Sukenik, S., Liu, Z., Lippincott-Schwartz., J. (2019). Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression. Nat. Cell biol., 21(12):1578-1589. DOI: 10.1038/s41556-019-0433-z; PMID: 31792379

21.  Ioannou, M.S.@, Jackson, J., Sheu, S.H., Chang, C.L., Weigel, A.V., Liu, H., Pasolli, H.A., Xu, S., Pang, S., Hess, H.F., Lippincott-Schwartz, J.@, Liu, Z.@ (2019). Neuron-astrocyte metabolic coupling protests against activity-induced fatty acid toxicity. Cell, 177(6):1522-1535. DOI: 10.1016/j.cell.2019.04.001; PMID: 31130380

20.  Yu, H., Yang, F., Dong, P., Liao, S., Liu, W.R., Zhao, G., Qin, B., Dou, Z., Liu, Z., Liu, W., Zang, J., Lippincott-Schwartz, J., Liu, X., Yao, X. (2019) NDP52 tunes cortical actin interaction with astral microtubules for accurate spindle orientation. Cell Research, 29(8):666-79. DOI: 10.1038/s41422-019-0189-9; PMID: 31201383

19.  Abdelfattah, A.S., Kawashima, T., Singh, A., Novak, O., Liu, H., Shuai, Y., Huang, Y.C., Campagnola, L., Seeman, S.C., Yu, J., Zheng, J., Grimm, J.B., Patel, R., Friedrich, J., Mensh, B.D., Paninski, L., Macklin, J.J., Murphy, G.J., Podgorski, K., Lin, B.J., Chen, T.W., Turner, G.C., Liu, Z., Koyama, M., Svoboda, K., Ahrens, M.B., Lavis, L.D., Schreiter, E.R. (2019). Bright and photostable chemigenetic indicators for extended in vivo voltage imaging. Science, 365(6454):699-704. DOI: 10.1126/science.aav6416; PMID: 31371562

18.  Chong, S., Dugast-Darzacq, C., Liu, Z., Dong, P., Dailey, G.M., Cattoglio, C., Heckert, A., Sambashiva, B., Lavis, L.D., Darzacq, X., Tjian, R. (2018). Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science, 361(6400). 10.1126/science.aar2555; PMID: 29930090

17.  Liu, H., Dong, P., Ioannou, M.S., Shea, J., Pasolli, A., Grimm, J., Rivlin, P., Lavis, L.D., Koyama, M., Liu, Z.@ (2018). Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling. Proc Natl Acad Sci U S A, 115(2):343-348. DOI: 10.1073/pnas.1713895115; PMID: 29284749

16.  Xie, L., Torigoe, S., H., Xiao, J., Mai, D.H., Li, L., Davis, F.P., Maire-Nelly, H., Grimm, J.B., Lavis, L.D., Darzacq, X., Cattoglio, C., Liu, Z.@  and Tjian, R.@ (2017). A dynamic interplay of Klf4 enhancer elments drives naïve-pluripotency. Genes & Development, 31(17):1795-1808. DOI: 10.1101/gad.303321.117; PMID: 28982762

15.  Kieffer-Kwon, K.R., Nimura, K., Rao, S.S.P., Xu, J., Jung, S., Pekowska, A., Dose, M., Stevens, E., Mathe, E., Dong, P., Huang, S.C., Ricci, M.A., Baranello, L., Zheng, Y., Tomassoni Ardori, F., Resch, W., Stavreva, D., Nelson, S., McAndrew, M., Casellas, A., Finn, E., Gregory, C., St Hilaire, B.G., Johnson, S.M., Dubois, W., Cosma, M.P., Batchelor, E., Levens, D., Phair, R.D., Misteli, T., Tessarollo, L., Hager, G., Lakadamyali, M.,  Liu, Z., Floer, M., Shroff, H., Aiden, E.L., Casellas, R. (2017). Myc regulates chromatin decompaction and nuclear architecture during B cell activation. Molecular Cell, 67(4):566-78. DOI: 10.1016/j.molcel.2017.07.013; PMID: 28803781

14.   Li, L., Liu, H., Dong, P., Li, D., Legant, W.R., Grimm, J.B., Lavis, L.D., Betzig, E., Tjian, R.@, Liu, Z.@  (2016). Real-time imaging of Huntingtin aggregates diverting target search and gene transcription. eLife, 5:e17056 DOI: 10.7554/eLife.17056; PMID: 27484239

13.  Grimm, J.B., English, B.P., Choi, H., Muthusamy, A.K., Mehl, B.P., Dong, P., Brown, T.A., Lippincott-Schwartz, J., Liu, Z., Lionnet, T., Lavis, L.D. (2016). Bright photoactivatable fluorophores for single-molecule imaging. Nature Methods, 13(12):985-988. DOI: 10.1038/nmeth.4034; PMID: 27776112

12.  Coleman, RA., Liu, Z., Darzacq, X., Tjian, R., Singer, RH., Lionnet, T. (2016). Imaging transcription: past, present and future. Cold Spring Harb Symp Quant Biol., pii: 027201. DOI: 10.1101/sqb.2015.80.027201; PMID: 26763984

11.  Knight, SC., Xie, L., Deng, W., Guglielmi, B., Bosanac, L., Witkowsky, LB., Zhang, ET., El-Beheiry, M., Dahan, M., Liu, Z.@, Doudna, JA.@, and Tjian, R.@ (2015). Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science, 350(6262):823-6. DOI: 10.1126/science.aac6572; PMID: 26564855

10.  Li, L., Martinez, SS., Hu, W., Liu, Z., Tjian, R. (2015). A specific E3 Ligase/deubiquitinase pair modulate TBP protein levels during muscle differentiation. eLife, 4:e0853. DOI: 10.7554/eLife.08536; PMID: 26393420

9.   Liu, Z.@, Legant, WR., Chen, B., Li, L., Grimm, JB., Lavis, LD., Betzig, E. and Tjian, R. (2014). 3D imaging of Sox2 enhancer clusters in embryonic stem cells. eLife, 3:e04236. 10.7554/eLife.04236; PMID: 25537195

8.    Chen, B., Legant, R.W., Wang, K., Shao, L., Milkie, D.E., Davidson, M.W., Janetopoulos, C., Wu, X.S., Hammer, J.A. 3rd, Liu, Z., English, B.P., Mimori-Kiyosue, Y., Romero, D.P., Ritter, A.T., Lippincott-Schwartz, J., Fritz-Laylin, L., Mullins, R.D., Mitchell, D.M., Bembenek, J.N., Reymann, A.C., Böhme, R., Grill, S.W., Wang, J.T., Seydoux, G., Tulu, U.S., Kiehart, D.P., Betzig, E. (2014). Lattice light sheet microscopy: imaging molecules, cells, and embryos at high spatiotemporal resolution. Science, 346(6208):1257998. DOI: 10.1126/science.1257998; PMID: 25342811

7.   Chen, J., Zhang, Z., Li, L., Chen, B., Revyakin, A., Hajj, B., Legant, W., Dahan, M., Lionnet, T., Betzig, E., Tjian, R., and Liu, Z.@ (2014). Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell, 156(6):1274-1285. DOI: 10.1016/j.cell.2014.01.062; PMID: 24630727

6.   Lolas, M., Valenzuela, P., Tjian, R.@, Liu, Z.@ (2014). Charting Brachyury-mediated developmental pathways during early mouse embryogenesis. Proc Natl Acad Sci U S A, 111(12):4478-83. DOI: 10.1073/pnas.1402612111; PMID: 24616493

Early work during training:

5.   Liu, Z.*, Scannell, D.R.*, Eisen, M.B., and Tjian, R. (2011). Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell, 146(5):720-31. (Cover story) DOI: 10.1016/j.cell.2011.08.005; PMID: 21884934

4.   Meng, Z., Liu, Z., Lou, Z., Gong, X., Cao, Y., Bartlam, M., Zhang, K., and Rao, Z. (2009). Purification, characterization and crystallization of pyrroline-5-carboxylate reductase from the hyperthermophilic archeon Sulfolobus Solfataricus. Protein Expr. Purif., 64(2):125-30. DOI: 10.1016/j.pep.2008.10.018; PMID: 19027071

3.   Meng, Z., Lou, Z., Liu, Z., Li, M., Zhao, X., Bartlam, M., and Rao, Z. (2006b). Crystal structure of human pyrroline-5-carboxylate reductase. J Mol. Biol., 359(5):1364-77. DOI: 10.1016/j.jmb.2006.04.053; PMID: 16730026

2.   Meng, Z., Lou, Z., Liu, Z., Hui, D., Bartlam, M., and Rao, Z. (2006a). Purification, characterization, and crystallization of human pyrroline-5-carboxylate reductase. Protein Expr. Purif., 49(1):83-7. DOI: 10.1016/j.pep.2006.02.019; PMID: 16600630

1.   Liu, Z., Lin, H., Ye, S., Liu, Q.Y., Meng, Z., Zhang, C.M., Xia, Y., Margoliash, E., Rao, Z., and Liu, X.J. (2006). Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis. Proc Natl Acad Sci U S A, 103(24):8965-70. DOI: 10.1073/pnas.0603327103; PMID: 16757556

b. Review articles, perspectives, and book chapters:

7.   Van, H.T., Xie, G., Dong, P., Liu, Z., Ge, K. (2024). KMT2 family of H3K4 methyltransferases: enzymatic activity-dependent and -independent functions. J. Mol. Biol., 436(7):168453. DOI: 10.1016/j.jmb.2024.168453; PMID: 38266981

6.   Xie, L.@ and Liu, Z.@ (2021). Single-cell imaging of genome organization and dynamics. Mol. Syst. Biol., 17(7):e9653. DOI: 10.15252/msb.20209653; PMID: 34232558

5.  Liu, Z.@ and Tjian, R.@ (2018). Visualizing transcription factor dynamics in single cells. Journal of Cell Biology, 217(4):1181-1191. DOI: 10.1083/jcb.201710038; PMID: 29378780

4.   Dong, P.@ and Liu, Z.@  (2017). Shaping development by stochasticity and dynamics in gene regulation. Open Biology, 7(5):170030. DOI: 10.1098/rsob.170030; PMID: 28469006

3.   Liu, Z.@ and Keller, P.@  (2016). Emerging imaging and genomic tools for systems developmental biology. Dev. Cell, 36(6):597-610. DOI: 10.1016/j.devcel.2016.02.016; PMID: 27003934

2.   Liu, Z.@ (2015). Lighting up genes in single cells at scale. Cell, 162(4):705-7. DOI: doi: 10.1016/j.cell.2015.07.052; PMID: 26276626

1.    Liu, Z.@, Lavis, LD.@, Betzig, E.@ (2015). Imaging live-cell dynamics and structure at the single-molecule Level. Molecular Cell, 58(4):644-59. DOI: doi.org/10.1016/j.molcel.2015.02.033; PMID: 26000849