Publications

Bolded names indicate Liu lab members.

DNA break induces rapid transcription repression mediated by proteasome-dependent RNAPII removal

He S, Huang Z, Liu Y, Ha T, Wu B

Cell Rep. 2024 Jul 23;43(7):114420. doi: 10.1016/j.celrep.2024.114420. Epub 2024 Jul 1. PMID: 38954517; PMCID: PMC11337244.

3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression

Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X,

Nat Commun. 2024 Jul 20;15(1):6130. doi: 10.1038/s41467-024-50387-w. PMID: 38328209; PMCID: PMC10849656.

A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies

Blake LA, Watkins L, Liu Y, Inoue T, Wu B.

Nat Commun. 2024 Mar 28;15(1):2720. doi: 10.1038/s41467-024-46943-z. PMID: 38548718; PMCID: PMC10979015.

Mapping cellular responses to DNA double-strand breaks using CRISPR technologies

Liu Y, Cottle WT, Ha T.

Trends Genet. 2023 Jul;39(7):560-574. doi: 10.1016/j.tig.2023.02.015. Epub 2023 Mar 25.PMID: 36967246

Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq

Zou RS, Liu Y, Gaido OER, Konig MF, Mog BJ, Shen LL, Aviles-Vazquez F, Marin-Gonzalez A, Ha T.

Nat Methods. 2023 May;20(5):706-713. doi: 10.1038/s41592-023-01840-z. Epub 2023 Apr 6.PMID: 37024653

Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites

Zou RS, Marin-Gonzalez A, Liu Y, Liu HB, Shen L, Dveirin RK, Luo JXJ, Kalhor R, Ha T.

Nat Cell Biol. 2022 Sep;24(9):1433-1444. Epub 2022 Sep 5. PubMed PMID: 36064968; PubMed Central PMCID: PMC9481459.

CRISPR deactivation in mammalian cells using photocleavable guide RNAs

Zou RS, Liu Y, Ha T.

STAR Protoc. 2021 Dec 17;2(4):100909. eCollection 2021 Dec 17. PubMed PMID: 34746867; PubMed Central PMCID: PMC8551926.

Cas9 deactivation with photocleavable guide RNAs

Zou RS, Liu Y, Wu B, Ha T.

Mol Cell. 2021 Apr 1;81(7):1553-1565.e8. Epub 2021 Mar 3. PubMed PMID: 33662274; PubMed Central PMCID: PMC8026597.

Very fast CRISPR on demand

Liu Y, Zou RS, He S, Nihongaki Y, Li X, Razavi S, Wu B, Ha T.

Science. 2020 Jun 12;368(6496):1265-1269. PubMed PMID: 32527834; PubMed Central PMCID: PMC7608738.

Forces during cellular uptake of viruses and nanoparticles at the ventral side

Wiegand T, Fratini M, Frey F, Yserentant K, Liu Y, Weber E, Galior K, Ohmes J, Braun F, Herten DP, Boulant S, Schwarz US, Salaita K, Cavalcanti-Adam EA, Spatz JP.

Nat Commun. 2020 Jan 2;11(1):32. PubMed PMID: 31896744; PubMed Central PMCID: PMC6940367.

Fluorescence Imaging Methods to Investigate Translation in Single Cells

Biswas J, Liu Y, Singer RH, Wu B.

Cold Spring Harb Perspect Biol. 2019 Apr 1;11(4). Review. PubMed PMID: 30082468; PubMed Central PMCID: PMC6442198.

Molecular Tension Probes to Investigate the Mechanopharmacology of Single Cells: A Step toward Personalized Mechanomedicine

Galior K, Ma VP, Liu Y, Su H, Baker N, Panettieri RA Jr, Wongtrakool C, Salaita K.

Adv Healthc Mater. 2018 Jul;7(14):e1800069. doi: 10.1002/adhm.201800069. Epub 2018 May 22. PubMed PMID: 29785773; PubMed Central PMCID: PMC6105437.

Light-Responsive Polymer Particles as Force Clamps for the Mechanical Unfolding of Target Molecules

Su H, Liu Z, Liu Y, Ma VP, Blanchard A, Zhao J, Galior K, Dyer RB, Salaita K.

Nano Lett. 2018 Apr 11;18(4):2630-2636. doi: 10.1021/acs.nanolett.8b00459. Epub 2018 Mar 28. PubMed PMID: 29589759; PubMed Central PMCID: PMC6110664.

Molecular Tension Probes for Imaging Forces at the Cell Surface.

Liu Y, Galior K, Ma VP, Salaita K.

Acc Chem Res. 2017 Dec 19;50(12):2915-2924. doi: 10.1021/acs.accounts.7b00305. Epub 2017 Nov 21. Review. PubMed PMID: 29160067; PubMed Central PMCID: PMC6066286.

Ratiometric Tension Probes for Mapping Receptor Forces and Clustering at Intermembrane Junctions

Ma VP, Liu Y, Blanchfield L, Su H, Evavold BD, Salaita K.

Nano Lett. 2016 Jul 13;16(7):4552-9. doi: 10.1021/acs.nanolett.6b01817. Epub 2016 Jun 2. PubMed PMID: 27192323; PubMed Central PMCID: PMC6061938.

DNA-based nanoparticle tension sensors reveal that T-cell receptors transmit defined pN forces to their antigens for enhanced fidelity

Liu Y, Blanchfield L, Ma VP, Andargachew R, Galior K, Liu Z, Evavold B, Salaita K.

Proc Natl Acad Sci U S A. 2016 May 17;113(20):5610-5. doi: 10.1073/pnas.1600163113. Epub 2016 May 2. PubMed PMID: 27140637; PubMed Central PMCID: PMC4878516.

Mechanically Induced Catalytic Amplification Reaction for Readout of Receptor-Mediated Cellular Forces

Ma VP, Liu Y, Yehl K, Galior K, Zhang Y, Salaita K.

Angew Chem Int Ed Engl. 2016 Apr 25;55(18):5488-92. doi: 10.1002/anie.201600351. Epub 2016 Apr 1. PubMed PMID: 27038115; PubMed Central PMCID: PMC5563213.

Nanoscale optomechanical actuators for controlling mechanotransduction in living cells

Liu Z, Liu Y, Chang Y, Seyf HR, Henry A, Mattheyses AL, Yehl K, Zhang Y, Huang Z, Salaita K.

Nat Methods. 2016 Feb;13(2):143-6. doi: 10.1038/nmeth.3689. Epub 2015 Dec 14. PubMed PMID: 26657558; PubMed Central PMCID: PMC4732909.

High-speed DNA-based rolling motors powered by RNase H

Yehl K, Mugler A, Vivek S, Liu Y, Zhang Y, Fan M, Weeks ER, Salaita K.

Nat Nanotechnol. 2016 Feb;11(2):184-90. doi: 10.1038/nnano.2015.259. Epub 2015 Nov 30. PubMed PMID: 26619152; PubMed Central PMCID: PMC4890967.

Titin-Based Nanoparticle Tension Sensors Map High-Magnitude Integrin Forces within Focal Adhesions

Galior K, Liu Y, Yehl K, Vivek S, Salaita K.

Nano Lett. 2016 Jan 13;16(1):341-8. doi: 10.1021/acs.nanolett.5b03888. Epub 2015 Dec 7. PubMed PMID: 26598972; PubMed Central PMCID: PMC5592801.

Nanoparticle tension probes patterned at the nanoscale: impact of integrin clustering on force transmission

Liu Y, Medda R, Liu Z, Galior K, Yehl K, Spatz JP, Cavalcanti-Adam EA, Salaita K.

Nano Lett. 2014 Oct 8;14(10):5539-46. doi: 10.1021/nl501912g. Epub 2014 Sep 30. PubMed PMID: 25238229; PubMed Central PMCID: PMC4189618.

Structurally defined nanoscale sheets from self-assembly of collagen-mimetic peptides

Jiang T, Xu C, Liu Y, Liu Z, Wall JS, Zuo X, Lian T, Salaita K, Ni C, Pochan D, Conticello VP.

J Am Chem Soc. 2014 Mar 19;136(11):4300-8. doi: 10.1021/ja412867z. Epub 2014 Mar 10. PubMed PMID: 24571053.

Quantum dots encapsulated within phospholipid membranes: phase-dependent structure, photostability, and site-selective functionalization

Zheng W, Liu Y, West A, Schuler EE, Yehl K, Dyer RB, Kindt JT, Salaita K.

J Am Chem Soc. 2014 Feb 5;136(5):1992-9. doi: 10.1021/ja411339f. Epub 2014 Jan 24. PubMed PMID: 24417287; PubMed Central PMCID: PMC3985776.

Tension sensing nanoparticles for mechano-imaging at the living/nonliving interface

Liu Y, Yehl K, Narui Y, Salaita K.

 J Am Chem Soc. 2013 Apr 10;135(14):5320-3. doi: 10.1021/ja401494e. Epub 2013 Mar 26. PubMed PMID: 23495954; PubMed Central PMCID: PMC3630457.

Real time observation of chemical reactions of individual metal nanoparticles with high-throughput single molecule spectral microscopy

Cheng J, Liu Y, Cheng X, He Y, Yeung ES.

Anal Chem. 2010 Oct 15;82(20):8744-9. doi: 10.1021/ac101933y. PubMed PMID: 20849132.