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Publications

L. Busto-Moner, J. Morival, H. Ren, A. Fahim, Z. Reitz, T. L. Downing, E. L. Read. Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation. PLOS Computational Biology doi.org/10.1371/journal.pcbi.1007195 (2020).

C. P. Gallivan, H. Ren, E. L. Read. Analysis of single-cell gene pair coexpression landscapes by stochastic kinetic modeling reveals gene-pair interactions in development. Frontiers in Genetics (2020).

K. Liu, B. K. Chu, J. Newby, E. L. Read, J. Lowengrub, J. Allard. Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length. PLoS Comput Biol 15(4): e1006352 (2019).

M. J. Tse, B. K. Chu, C. P. Gallivan, E. L. Read. Rare-event sampling of epigenetic landscapes and phenotype transitions. PLOS Computational Biology 14(8): e1006336 (2018).

B. K. Chu, M. J. Tse, R. R. Sato, E. L. Read. Markov State Models of gene regulatory networks. BMC Systems Biology 11:14 (2017).

Y. Vodovotz, A. Xia, E. L. Read, J. Bassaganya-Riera, D. A. Hafler, E. Sontag, J. Wang, J. S. Tsang, J. D. Day, S. H. Kleinstein, A. J. Butte, M. C. Altman, R. Hammond, S. C. Sealfon. Solving Immunology? Trends in Immunology 38(2) (2017).

T. D. Smith, M. J. Tse, E. L. Read, W. F. Liu. Regulation of macrophage polarization and plasticity by complex activation signals. Integr. Biol. 8, 946-955 (2016).

M. J. Tse, B. K. Chu, M. Roy, E. L. Read. DNA-binding kinetics determines mechanism of noise-induced switching in gene networks, Biophys. J. 109(8), 1746-1757 (2015). Named a Best of 2015 article

E. L. Read, A. A. Tovo-Dwyer, A. K. Chakraborty. Stochastic effects are important in intrahost HIV evolution even when viral loads are high. Proc. Natl. Acad. Sci. 109, 19727-19732 (2012).

A. Košmrlj*, E. L. Read*, Y. Qi, T. M. Allen, M. Altfeld, S. G. Deeks, F. Pereyra, M. Carrington, B. D. Walker, A. K. Chakraborty. Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature 465, 350-354 (2010).

G. S. Schlau-Cohen, T. R. Calhoun, N.S. Ginsberg, E. L. Read, M. Ballottari, R. Bassi, R. van Grondelle, G. R. Fleming. Pathways of energy flow in LHCII from two-dimensional electronic spectroscopy. J. Phys. Chem. B 113, 15352-15363 (2009).

E. L. Read, H. Lee, G. R. Fleming. Photon echo studies of photosynthetic light harvesting. Photos. Res. 101, 233-243 (2009).

E. L. Read, G. S. Schlau-Cohen, G. S. Engel, T. Georgiou, M. Z. Papiz, G. R. Fleming. Pigment organization and energy level structure in Light-harvesting Complex 4: Insights from two-dimensional electronic spectroscopy. J. Phys. Chem. B 113, 6495-6504 (2009).

E. L. Read, G. S. Schlau-Cohen, G. S. Engel, R. E. Blankenship, G. R. Fleming. Visualization of excitonic structure in the Fenna-Matthews-Olson photosynthetic complex by polarization-dependent two-dimensional electronic spectroscopy. Biophys. J. 95, 847-856 (2008).

D. Zigmantas, Y.-Z. Ma, E. L. Read, G. R. Fleming. Nonlinear femtosecond optical spectroscopy techniques in photosynthesis. In: Biophysical Techniques in Photosynthesis, Vol. II, T. J. Aartsma and J. Matysik, eds. Springer, 201-222 (2008).

E. L. Read*, G. S. Engel*, T. R. Calhoun, T. Mančal, T. K. Ahn, R. E. Blankenship, and G. R. Fleming. Cross-peak-specific two-dimensional electronic spectroscopy. Proc. Natl. Acad. Sci. 104, 14203-14208 (2007).

G. S. Engel, T. R. Calhoun, E. L. Read, T. K. Ahn, T. Mančal, Y.-C. Cheng, R. E. Blankenship, G. R. Fleming. Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446, 782-786 (2007).

C. W. Blackledge, J. M. Szarko, A. Dupont, G. H. Chan, E. L. Read, S. R. Leone. Zinc oxide nanorod growth on gold islands prepared by microsphere lithography on silicon and quartz. J. Nanosci. Nanotech. 7, 3336-3339 (2007).

D. Zigmantas, E. L. Read, T. Mančal, T. Brixner, A. T. Gardiner, R. J. Cogdell, and G. R. Fleming.Two-dimensional electronic spectroscopy of the B800–B820 light-harvesting complex. Proc. Natl. Acad. Sci. 103, 12672-12677 (2006).

*equal contributors