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Zhe J. Liu, Ph.D. - Publications

Affiliations: 
Janelia Research Campus 
Area:
gene regulation; membrane localized proteins
Website:
https://www.janelia.org/people/zhe-j-liu
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Dong P, Zhang S, Gandin V, Xie L, Wang L, Lemire AL, Li W, Otsuna H, Kawase T, Lander AD, Chang HY, Liu ZJ. Cohesin prevents cross-domain gene coactivation. Nature Genetics. PMID 39048795 DOI: 10.1038/s41588-024-01852-1  0.348
2024 Yang LZ, Min YH, Liu YX, Gao BQ, Liu XQ, Huang Y, Wang H, Yang L, Liu ZJ, Chen LL. CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells. Nature Methods. PMID 38965442 DOI: 10.1038/s41592-024-02333-3  0.355
2024 Hao S, Lee YJ, Benhamou Goldfajn N, Flores E, Liang J, Fuehrer H, Demmerle J, Lippincott-Schwartz J, Liu Z, Sukenik S, Cai D. YAP condensates are highly organized hubs. Iscience. 27: 109927. PMID 38784009 DOI: 10.1016/j.isci.2024.109927  0.632
2024 Holland KL, Plutkis SE, Daugird TA, Sau A, Grimm JB, English BP, Zheng Q, Dave S, Rahman F, Xie L, Dong P, Tkachuk AN, Brown TA, Singer RH, Liu Z, et al. A series of spontaneously blinking dyes for super-resolution microscopy. Biorxiv : the Preprint Server For Biology. PMID 38766149 DOI: 10.1101/2024.02.23.581625  0.754
2024 Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nature Communications. 15: 4178. PMID 38755200 DOI: 10.1038/s41467-024-48562-0  0.331
2024 Van HT, Xie G, Dong P, Liu Z, Ge K. KMT2 Family of H3K4 Methyltransferases: Enzymatic Activity-dependent and -independent Functions. Journal of Molecular Biology. 168453. PMID 38266981 DOI: 10.1016/j.jmb.2024.168453  0.526
2023 Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Biorxiv : the Preprint Server For Biology. PMID 38014222 DOI: 10.1101/2023.11.09.566470  0.328
2023 Grimm JB, Tkachuk AN, Patel R, Hennigan ST, Gutu A, Dong P, Gandin V, Osowski AM, Holland KL, Liu ZJ, Brown TA, Lavis LD. Optimized Red-Absorbing Dyes for Imaging and Sensing. Journal of the American Chemical Society. 145: 23000-23013. PMID 37842926 DOI: 10.1021/jacs.3c05273  0.509
2023 Liu Y, Huang Z, Liu H, Ji Z, Arora A, Cai D, Wang H, Liu M, Simko EAJ, Zhang Y, Periz G, Liu Z, Wang J. DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat. Neuron. 111: 1345. PMID 37080168 DOI: 10.1016/j.neuron.2023.03.035  0.416
2023 Liu Y, Huang Z, Liu H, Ji Z, Arora A, Cai D, Wang H, Liu M, Simko EAJ, Zhang Y, Periz G, Liu Z, Wang J. DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat. Neuron. PMID 36822200 DOI: 10.1016/j.neuron.2023.01.022  0.514
2023 Bonello TT, Cai D, Fletcher GC, Wiengartner K, Pengilly V, Lange KS, Liu Z, Lippincott-Schwartz J, Kavran JM, Thompson BJ. Phase separation of Hippo signalling complexes. The Embo Journal. e112863. PMID 36807601 DOI: 10.15252/embj.2022112863  0.58
2022 Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, ... Liu Z, et al. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nature Genetics. PMID 36123406 DOI: 10.1038/s41588-022-01177-x  0.728
2022 Xie L, Dong P, Qi Y, Hsieh TS, English BP, Jung S, Chen X, De Marzio M, Casellas R, Chang HY, Zhang B, Tjian R, Liu Z. BRD2 compartmentalizes the accessible genome. Nature Genetics. 54: 481-491. PMID 35410381 DOI: 10.1038/s41588-022-01044-9  0.751
2021 Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong IT, Wu S, Dehkordi SR, ... ... Liu Z, et al. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature. PMID 34819668 DOI: 10.1038/s41586-021-04116-8  0.769
2021 McCann AJ, Lou J, Moustaqil M, Graus MS, Blum A, Fontaine F, Liu H, Luu W, Rudolffi-Soto P, Koopman P, Sierecki E, Gambin Y, Meunier FA, Liu Z, Hinde E, et al. A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity. Nucleic Acids Research. PMID 34570228 DOI: 10.1093/nar/gkab820  0.345
2021 Xie L, Liu Z. Single-cell imaging of genome organization and dynamics. Molecular Systems Biology. 17: e9653. PMID 34232558 DOI: 10.15252/msb.20209653  0.75
2021 Grimm JB, Xie L, Casler JC, Patel R, Tkachuk AN, Falco N, Choi H, Lippincott-Schwartz J, Brown TA, Glick BS, Liu Z, Lavis LD. A General Method to Improve Fluorophores Using Deuterated Auxochromes. Jacs Au. 1: 690-696. PMID 34056637 DOI: 10.1021/jacsau.1c00006  0.739
2021 Cai D, Liu Z, Lippincott-Schwartz J. Biomolecular Condensates and Their Links to Cancer Progression. Trends in Biochemical Sciences. PMID 33579564 DOI: 10.1016/j.tibs.2021.01.002  0.573
2020 Grimm JB, Tkachuk AN, Xie L, Choi H, Mohar B, Falco N, Schaefer K, Patel R, Zheng Q, Liu Z, Lippincott-Schwartz J, Brown TA, Lavis LD. A general method to optimize and functionalize red-shifted rhodamine dyes. Nature Methods. PMID 32719532 DOI: 10.1038/S41592-020-0909-6  0.762
2020 Binns TC, Ayala AX, Grimm JB, Tkachuk AN, Castillon GA, Phan S, Zhang L, Brown TA, Liu Z, Adams SR, Ellisman MH, Koyama M, Lavis LD. Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems. Cell Chemical Biology. PMID 32698018 DOI: 10.1016/J.Chembiol.2020.07.001  0.323
2020 Matthies D, Lee NYJ, Gatera I, Pasolli HA, Zhao X, Liu H, Walpita D, Liu Z, Yu Z, Ioannou MS. Microdomains form on the luminal face of neuronal extracellular vesicle membranes. Scientific Reports. 10: 11953. PMID 32686698 DOI: 10.1038/S41598-020-68436-X  0.594
2020 Ochiai H, Hayashi T, Umeda M, Yoshimura M, Harada A, Shimizu Y, Nakano K, Saitoh N, Liu Z, Yamamoto T, Okamura T, Ohkawa Y, Kimura H, Nikaido I. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. Science Advances. 6: eaaz6699. PMID 32596448 DOI: 10.1126/Sciadv.Aaz6699  0.411
2020 Lerner J, Gomez-Garcia PA, McCarthy RL, Liu Z, Lakadamyali M, Zaret KS. Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin. Molecular Cell. PMID 32574554 DOI: 10.1016/J.Molcel.2020.05.036  0.358
2020 Xie L, Dong P, Chen X, Hsieh TS, Banala S, De Marzio M, English BP, Qi Y, Jung SK, Kieffer-Kwon KR, Legant WR, Hansen AS, Schulmann A, Casellas R, Zhang B, ... ... Liu Z, et al. 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature Methods. PMID 32203384 DOI: 10.1038/S41592-020-0775-2  0.758
2019 Piccolo FM, Liu Z, Dong P, Hsu CL, Stoyanova EI, Rao A, Tjian R, Heintz N. MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions. Elife. 8. PMID 31868585 DOI: 10.7554/Elife.51449  0.683
2019 Cai D, Feliciano D, Dong P, Flores E, Gruebele M, Porat-Shliom N, Sukenik S, Liu Z, Lippincott-Schwartz J. Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression. Nature Cell Biology. PMID 31792379 DOI: 10.1038/S41556-019-0433-Z  0.742
2019 Ioannou MS, Liu Z, Lippincott-Schwartz J. A Neuron-Glia Co-culture System for Studying Intercellular Lipid Transport. Current Protocols in Cell Biology. 84: e95. PMID 31483110 DOI: 10.1002/Cpcb.95  0.646
2019 Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, Huang YC, Campagnola L, Seeman SC, Yu J, Zheng J, Grimm JB, Patel R, Friedrich J, Mensh BD, ... ... Liu Z, et al. Bright and photostable chemigenetic indicators for extended in vivo voltage imaging. Science (New York, N.Y.). PMID 31371562 DOI: 10.1126/Science.Aav6416  0.409
2019 Yu H, Yang F, Dong P, Liao S, Liu WR, Zhao G, Qin B, Dou Z, Liu Z, Liu W, Zang J, Lippincott-Schwartz J, Liu X, Yao X. NDP52 tunes cortical actin interaction with astral microtubules for accurate spindle orientation. Cell Research. PMID 31201383 DOI: 10.1038/S41422-019-0189-9  0.626
2019 Ioannou MS, Jackson J, Sheu SH, Chang CL, Weigel AV, Liu H, Pasolli HA, Xu CS, Pang S, Matthies D, Hess HF, Lippincott-Schwartz J, Liu Z. Neuron-Astrocyte Metabolic Coupling Protects against Activity-Induced Fatty Acid Toxicity. Cell. PMID 31130380 DOI: 10.1016/J.Cell.2019.04.001  0.654
2019 Piccolo FM, Liu Z, Dong P, Hsu C, Stoyanova EI, Rao A, Tjian R, Heintz N. Author response: MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions Elife. DOI: 10.7554/Elife.51449.Sa2  0.308
2018 Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, Tjian R. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science (New York, N.Y.). PMID 29930090 DOI: 10.1126/Science.Aar2555  0.75
2018 Liu Z, Tjian R. Visualizing transcription factor dynamics in living cells. The Journal of Cell Biology. PMID 29378780 DOI: 10.1083/Jcb.201710038  0.638
2018 Liu Z. Decision letter: Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity Elife. DOI: 10.7554/Elife.41769.053  0.36
2017 Liu H, Dong P, Ioannou MS, Li L, Shea J, Pasolli HA, Grimm JB, Rivlin PK, Lavis LD, Koyama M, Liu Z. Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling. Proceedings of the National Academy of Sciences of the United States of America. PMID 29284749 DOI: 10.1073/Pnas.1713895115  0.738
2017 Xie L, Torigoe SE, Xiao J, Mai DH, Li L, Davis FP, Dong P, Marie-Nelly H, Grimm J, Lavis L, Darzacq X, Cattoglio C, Liu Z, Tjian R. A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency. Genes & Development. 31: 1795-1808. PMID 28982762 DOI: 10.1101/Gad.303321.117  0.756
2017 Kieffer-Kwon KR, Nimura K, Rao SSP, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Ardori FT, ... ... Liu Z, et al. Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Molecular Cell. PMID 28803781 DOI: 10.1016/J.Molcel.2017.07.013  0.613
2017 Dong P, Liu Z. Shaping development by stochasticity and dynamics in gene regulation. Open Biology. 7. PMID 28469006 DOI: 10.1098/Rsob.170030  0.588
2016 Grimm JB, English BP, Choi H, Muthusamy AK, Mehl BP, Dong P, Brown TA, Lippincott-Schwartz J, Liu Z, Lionnet T, Lavis LD. Bright photoactivatable fluorophores for single-molecule imaging. Nature Methods. PMID 27776112 DOI: 10.1038/Nmeth.4034  0.666
2016 Li L, Liu H, Dong P, Li D, Legant WR, Grimm JB, Lavis LD, Betzig E, Tjian R, Liu Z. Real-time imaging of Huntingtin aggregates diverting target search and gene transcription. Elife. 5. PMID 27484239 DOI: 10.7554/Elife.17056  0.715
2016 Liu Z, Keller PJ. Emerging Imaging and Genomic Tools for Developmental Systems Biology. Developmental Cell. 36: 597-610. PMID 27003934 DOI: 10.1016/J.Devcel.2016.02.016  0.406
2016 Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, ... ... Liu Z, ... ... Liu Z, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 12: 1-222. PMID 26799652 DOI: 10.1080/15548627.2015.1100356  0.424
2016 Coleman RA, Liu Z, Darzacq X, Tjian R, Singer RH, Lionnet T. Imaging Transcription: Past, Present, and Future. Cold Spring Harbor Symposia On Quantitative Biology. PMID 26763984 DOI: 10.1101/Sqb.2015.80.027201  0.62
2016 Li L, Liu H, Dong P, Li D, Legant WR, Grimm JB, Lavis LD, Betzig E, Tjian R, Liu Z. Author response: Real-time imaging of Huntingtin aggregates diverting target search and gene transcription Elife. DOI: 10.7554/Elife.17056.034  0.538
2016 Wong V, Liu Z, Peng S, Kenworthy C, Liu W, Coleman RA. Single Molecule Imaging of p53's Dynamic Interaction with Chromatin Biophysical Journal. 110: 516. DOI: 10.1016/J.Bpj.2015.11.2758  0.361
2015 Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science (New York, N.Y.). 350: 823-6. PMID 26564855 DOI: 10.1126/Science.Aac6572  0.789
2015 Li L, Martinez SS, Hu W, Liu Z, Tjian R. A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation. Elife. 4. PMID 26393420 DOI: 10.7554/Elife.08536  0.53
2015 Liu Z. Lighting Up Genes in Single Cells at Scale. Cell. 162: 705-7. PMID 26276626 DOI: 10.1016/J.Cell.2015.07.052  0.346
2015 Liu Z, Lavis LD, Betzig E. Imaging live-cell dynamics and structure at the single-molecule level. Molecular Cell. 58: 644-59. PMID 26000849 DOI: 10.1016/J.Molcel.2015.02.033  0.379
2015 Liu Z, Lavis LD, Betzig E. Imaging Live-Cell Dynamics and Structure at the Single-Molecule Level Molecular Cell. 58: 644. DOI: 10.1016/j.molcel.2015.02.033  0.393
2014 Liu Z, Legant WR, Chen BC, Li L, Grimm JB, Lavis LD, Betzig E, Tjian R. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. Elife. 3: e04236. PMID 25537195 DOI: 10.7554/Elife.04236  0.596
2014 Chen BC, Legant WR, Wang K, Shao L, Milkie DE, Davidson MW, Janetopoulos C, Wu XS, Hammer JA, Liu Z, English BP, Mimori-Kiyosue Y, Romero DP, Ritter AT, Lippincott-Schwartz J, et al. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science (New York, N.Y.). 346: 1257998. PMID 25342811 DOI: 10.1126/Science.1257998  0.577
2014 Chen J, Zhang Z, Li L, Chen BC, Revyakin A, Hajj B, Legant W, Dahan M, Lionnet T, Betzig E, Tjian R, Liu Z. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell. 156: 1274-85. PMID 24630727 DOI: 10.1016/J.Cell.2014.01.062  0.594
2014 Lolas M, Valenzuela PD, Tjian R, Liu Z. Charting Brachyury-mediated developmental pathways during early mouse embryogenesis. Proceedings of the National Academy of Sciences of the United States of America. 111: 4478-83. PMID 24616493 DOI: 10.1073/Pnas.1402612111  0.584
2014 Liu Z, Legant WR, Chen B, Li L, Grimm JB, Lavis LD, Betzig E, Tjian R. Author response: 3D imaging of Sox2 enhancer clusters in embryonic stem cells Elife. DOI: 10.7554/Elife.04236.035  0.51
2011 Liu Z, Scannell DR, Eisen MB, Tjian R. Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell. 146: 720-31. PMID 21884934 DOI: 10.1016/J.Cell.2011.08.005  0.595
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