Our full list of publications is at Google Scholar.

A Privacy-Preserving COVID-19 Symptom Tracker with 3.6 Million Reports
A. Ranjan, S. Li, B. Chen, A. Chiu, K. Jagadeesh and J. Liphardt
medRxiv (2020) [Full]

NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded Cells
L. Yang, RP. Ghosh , JM. Franklin, S. Chen, C. You, RR. Narayan, ML. Melcher and Jan T. Liphardt
PLoS Computational Biology 16(9): e1008193 (2020) [Full]

Concerted localization resets precede YAP-dependent transcription
JM. Franklin, RP. Ghosh, Q. Shi, Jan T. Liphardt
Nature Communications 11: 4581 (2020) [Full]

A fluorogenic array for temporally unlimited single-molecule tracking
RP. Ghosh, JM. Franklin, WE. Draper, Q. Shi, B. Beltran, AJ. Spakowitz and J. Liphardt
Nature Chemical Biology 15, 401-409 (2019) [Full]

A Mutation in Histone H2B Represents a New Class of Oncogenic Driver.
Bennett RL, Bele A, Small EC, Will CM, Nabet B, Oyer JA, Huang X, Ghosh RP, Grzybowski AT, Yu T, Zhang Q, Riva A, Lele TP, Schatz GC, Kelleher NL, Ruthenburg AJ, Liphardt J, Licht JD
Cancer Discov. 2019 [Full]

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions
Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT.
Nat Commun. 10(1), 3221 (2019) [Full]

Physical confinement induces malignant transformation in mammary epithelial cells
Lu YC, Chu T, Hall MS, Fu DJ, Shi Q, Chiu A, An D, Wang LH, Pardo Y, Southard T, Danko CG, Liphardt J, Nikitin AY, Wu M, Fischbach C, Coonrod S, Ma M.
Biomaterials (2019) [Full]

Strong triaxial coupling and anomalous Poisson effect in collagen networks
Ban E, Wang H, Franklin JM, Liphardt JT, Janmey PA, Shenoy VB.
PNAS 116(14), 6790-6799 (2019) [Full]

Mechanisms of Plastic Deformation in Collagen Networks Induced by Cellular Forces
Ehsan Ban, J. Matthew Franklin, Sungmin Nam, Lucas R. Smith, Hailong Wang, Rebecca G. Wells, Ovijit Chaudhuri, Jan T. Liphardt, Vivek B. Shenoy
Biophys J. 539049 (2018) [Full]

Origins of chemoreceptor curvature sorting in Escherichia coli
WE. Draper and J. Liphardt
Nature Communications 8, 14838 (2017) [Full]

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing
X. Chen, Y. Shen, WE. Draper, JD. Buenrostro, U. Litzenburger, SW. Cho, AT. Satpathy, AC. Carter, RP. Ghosh, A. East-Seletsky, JA. Doudna, WJ. Greenleaf, J. Liphardt, and HY. Chang
Nature Methods 13, 1013–1020 (2016) [Full]

Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner
AR. Lowe, JH. Tang, J. Yassif, M. Graf, WYC. Huang, JT. Groves, K. Weis, and J. Liphardt
eLife 04052, (2015) [Full]

Rapid disorganization of mechanically interacting systems of mammary acini
Q. Shi, RP. Ghosh, H. Engelke, CH. Rycroft, L. Cassereau, JA. Sethian, VM. Weaver, and J. Liphardt
PNAS 111(2), 658-663 (2014) [Full]
Selected as the PNAS featured image.

Scaffold nucleoporins Nup188 and Nup192 are structurally related to nuclear transport receptors
K. Andersen, E. Onischenko, J. Tang, P. Kumar, J. Chen, J. Liphardt, K. Weis, and T. Schwartz
eLife 00745, (2013) [Full]

Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms
V. Berk, JCN. Fong, GT. Dempsey, ON. Develioglu, X. Zhuang, J. Liphardt, FH. Yildiz, and S. Chu
Science 337, 236-239 (2012) [Full]
Science Editor's summary.

News and Views. Single molecules: Thermodynamic limits
J. Liphardt
Nature Physics 8, 638–639 (2012) [Full]

Scanning angle interference microscopy reveals cell dynamics at the nanoscale
MJ. Paszek, CC. DuFort, MG. Rubashkin, MW. Davidson, KS. Thorn, J. Liphardt, and VM. Weaver
Nature Methods 9, 825-827 (2012) [Full]

Selectivity Mechanism of the Nuclear Pore Complex Characterized by Single Cargo Tracking
AR. Lowe, JJ. Siegel, P. Kalab, M. Sui, K. Weis, and J. Liphardt
Nature 467, 600-603 (2010) [PDF]

Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy
D. Greenfield, AL. McEvoy, H. Shroff, GE. Crooks, NS. Wingreen, E. Betzig, and J. Liphardt
PLoS Biology 7, e1000137 (2009) [PDF]
Science Editors' Choice commentary and Nature Chemical Biology Research Highlight.

Tunable nanowire nonlinear optical probe
Y. Nakayama, PJ. Pauzauskie, A. Radenovic, RM. Onorato, RJ. Saykally, J. Liphardt, and P. Yang
Nature 447, 1098-1101 (2007) [Full]
Cover article.

Use of Plasmon Coupling to Reveal the Dynamics of DNA Bending and Cleavage by Single EcoRV Restriction Enzymes
B. Reinhard, S. Sheikholeslami, A. Mastroianni, AP. Alivisatos, and J. Liphardt
PNAS 104, 2667-2672 (2007) [Full]

Light-powering Escherichia coli with proteorhodopsin
JM. Walter, D. Greenfield, CJ. Bustamante, and J. Liphardt
PNAS 104, 2408-2412 (2007) [Full]

Optical Trapping and Integration of Semiconductor Nanowire Assemblies in Water
PJ. Pauzauskie, A. Radenovic, E. Trepagnier, H. Shroff, P. Yang, and J. Liphardt
Nature Materials 5, 97–101 (2006) [Full]

Biocompatible force sensor with optical readout and dimensions of 6 nm3
H. Shroff, BM. Reinhard, M. Siu, H. Agarwal, A. Spakowitz, and J. Liphardt
Nano Letters 5, 1509-1514 (2005) [Full]

A Molecular Ruler Based on Plasmon Coupling of Single Gold and Silver Nanoparticles
C. Sönnichsen, B. Reinhard, J. Liphardt, and AP. Alivisatos
Nature Biotechnology 23, 741-745 (2005) [Full]
Science News of the Week coverage.

Experimental Test of Hatano and Sasa's Nonequilibrium Steady-state Equality
EH. Trepagnier, C. Jarzynski, F. Ritort, GE. Crooks, CJ. Bustamante, and J. Liphardt
PNAS 101, 15038-15041 (2004) [Full]

Identifying Kinetic Barriers to Mechanical Unfolding of the T. thermophila Ribozyme
B. Onoa, S. Dumont, J. Liphardt, SB. Smith, I. Tinoco, Jr., and CJ. Bustamante
Science 299, 1892-1895 (2003) [Full]

Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality
J. Liphardt, S. Dumont, SB. Smith, I. Tinoco, Jr., and CJ. Bustamante
Science 296, 1832-1835 (2002) [Full]

Reversible Unfolding of Single RNA Molecules Using Mechanical Force
J. Liphardt, B. Onoa, SB. Smith, I. Tinoco, Jr., and CJ. Bustamante
Science 292, 733-737 (2001) [PDF]
Science Perspectives commentary with some nice pictures by J. Fernandez, S. Chu and A. Oberhauser.

Reviews and Commentaries

What does physics have to do with cancer?
F. Michor, J. Liphardt, M. Ferrari, and J. Widom
Nature Reviews Cancer 11, 657-670 (2011) [PDF]
Cover article.

Q & A: Single-molecule localization microscopy for biological imaging
AL. McEvoy, D. Greenfield, M. Bates, and J. Liphardt
BMC Biology 8, (2010) [PDF]

Potential of light-harvesting proton pumps for bioenergy applications
JM Walter, D. Greenfield, and J. Liphardt
Curr. Opin. Biotechnol. 21, (2010) [Full]

The Great Hunt For Extra Compliance
J. Liphardt
Biophysical Journal 93, 4099 (2007) [Full]

The Nonequilibrium Thermodynamics of Small Systems
F. Ritort, J. Liphardt, and C. Bustamante
Physics Today, July (2005) [Full]

Single Molecule Studies of DNA Mechanics
CJ. Bustamante, SB. Smith, J. Liphardt, and D. Smith
Curr. Opin. Struct. Biol. 10, 279-285 (2000) [Full]

Typos, Errors, and Notes

Science 292. Eq. 3 is missing a minus sign - it should be e-(ko km/br)*e(bF-1). Also, the equation in the legend to figure 2 should be p(E)=1/(1 + eE/kT). The paper was originally quite long, and we moved a lot of stuff to a web supplement.

PNAS 104. Plasmon rulers paper. The units of the timescales in Figure 3, panels e-h, are wrong - they should be s and not ms. Panels a-d are correct.

PNAS 104. Proteorhodopsin paper. Supporting Information equation 9 is incorrect. The right side of the expression should be inverted.