Publications

Highlights

(For a full list see below or go to Google Scholar)

Theory of active chromatin remodeling

Using a perturbation theory, we show that the non-equilibrium impact of remodeling enzymes on nucleosome positioning can be well approximated by eective equilibrium models with rescaled temperatures and interactions. Numerical simulations support the accuracy of the theory in predicting both kinetic and steady-state quantities, including the eective temperature and the radial distribution function.

Zhongling Jiang, Bin Zhang

PRL, 123, 208102 (2019)

Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins

Here, we present a generic algorithm to improve the accuracy of coarse-grained IDP models using a diverse set of experimental measurements. We successfully applied the algorithm to derive a transferable force field, which we term as MOFF, for de novo prediction of IDP structures.

Andrew P Latham, Bin Zhang

JCTC, 16, 773 (2019)

Predicting three-dimensional genome organization with chromatin states

We introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution.

Yifeng Qi, Bin Zhang

PLoS Comp Bio, 15, e1007024 (2019)

 

Full List

* indicates co-corresponding authors.

Submitted

Phosphorylation-dependent conformations of the disordered carboxyl-terminus domain in EGFR
Raju Regmi, Shwetha Srinivasan, Vandna Kukshal, Andrew P. Latham, Weidong Cui, Bin Zhang, Ron Bose, Gabriela S. Schlau-Cohen

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Xinqiang Ding, Xingcheng Lin, and Bin Zhang

Computing Absolute Free Energy with Deep Generative Models
Xinqiang Ding, Bin Zhang
arXiv

On the role of transcription in positioning nucleosomes
Zhongling Jiang, Bin Zhang
bioRxiv

Data-driven polymer model for mechanistic exploration of diploid genome organization
Yifeng Qi, Alejandro Reyes, Sarah E Johnstone, Martin J Aryee, Bradley E Bernstein, Bin Zhang
bioRxiv

Characterizing chromatin folding coordinate and landscape with deep learning
Wen Jun Xie, Yifeng Qi, Bin Zhang
bioRxiv

PRC2 bridges non-adjacent nucleosomes to establish heterochromatin
Rachel Leicher, J Ge Eva, Xingcheng Lin, Matthew J Reynolds, Thomas Walz, Bin Zhang*, Tom W Muir, Shixin Liu*
bioRxiv

Super-resolution imaging reveals 3D structure and organizing mechanism of accessible chromatin
Liangqi Xie, Peng Dong, Yifeng Qi, Margherita De Marzio, Xingqi Chen, Sambashiva Banala, Wesley R Legant, Brian P English, Anders S Hansen, Anton Schulmann, Luke D Lavis, Eric Betzig, Rafael Casellas, Howard Y Chang, Bin Zhang*, Robert Tjian*, Zhe Liu*
bioRxiv

Intracellular compaction induced by extracellular ligand-binding in epidermal growth factor receptor
Shwetha Srinivasan, Raju Regmi, Xingcheng Lin, Steven D. Quinn, Wei He, Kermit L. Carraway, III, Matthew A. Coleman, Bin Zhang*, Gabriela S. Schlau-Cohen*

2020

Structural and Dynamic Features of N-glycosylated Human RNase1
Henry Kilgore, Andrew Latham, Valerie Ressler, Bin Zhang*, Ronald T. Raines*
Biochemistry, in press

A survey of genome topology in colorectal cancer reveals large-scale compartmental changes that restrain malignant progression
Sarah E. Johnstone, Alejandro Reyes, Yifeng Qi, Esmat Hegazi, Karin Pelka, Jonathan Chen, Luli Zou, Yotam Drier, Vivian Hecht, Noam Shoresh, Caleb Lareau, Sowmya Iyer, Nir Hacohen, Rafael Irizarry, Bin Zhang, Martin J. Aryee, Bradley E. Bernstein
Cell, in press

3D ATAC-PALM: super-resolution imaging of the accessible genome
Xie, Liangqi, Dong, Peng, Chen, Xingqi, Hsieh, Tsung-Han S., Banala, Sambashiva, De Marzio, Margherita, English, Brian P., Qi, Yifeng, Jung, Seol Kyoung, Kieffer-Kwon, Kyong-Rim, Legant, Wesley R., Hansen, Anders S., Schulmann, Anton, Casellas, Rafael, Zhang, Bin, Betzig, Eric, Lavis, Luke D., Chang, Howard Y., Tjian, Robert, Liu, Zhe
Nat Met, 17, 430 (2020)

Quantifying Epigenetic Stability with Minimum Action Paths
Amogh Sood, Bin Zhang
Phys. Rev. E, 101, 062409 (2020)

2019

Theory of active chromatin remodeling
Zhongling Jiang, Bin Zhang
PRL, 123, 208102 (2019)

Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins
Andrew P Latham, Bin Zhang
JCTC, 16, 773 (2019)

Predicting three-dimensional genome organization with chromatin states
Yifeng Qi, Bin Zhang
PLoS Comp Bio, 15, e1007024 (2019)

Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals
Jorge L Rosa-Raíces, Bin Zhang, Thomas F Miller III
JCP, 151, 164120 (2019)

Learning the formation mechanism of domain-Level chromatin states with epigenomics data
Wen Jun Xie, Bin Zhang
Biophys J, 116, 2047 (2019)

Critical role of histone tail entropy in nucleosome unwinding
Thomas Parsons, Bin Zhang
JCP, 150, 185103 (2019)

Learning genomic energy landscapes from experiments
MICHELE Di Pierro, RYAN R Cheng, B Zhang, JOSÉ N Onuchic, PETER G Wolynes
Book Chapter, CRC Press, 305 (2019)

Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data
Andrew P Latham, Bin Zhang
JPCB, 123, 1026 (2019)

Before MIT

Genomic energy landscapes
Bin Zhang, Peter G Wolynes
Biophys J, 112, 427 (2017)

Transferable model for chromosome architecture
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, Peter G Wolynes, José N Onuchic
PNAS, 113, 12168 (2016)

Molecular mechanism of facilitated dissociation of Fis protein from DNA
Min-Yeh Tsai, Bin Zhang, Weihua Zheng, Peter G Wolynes
JACS, 138, 13497 (2016)

A link between integral membrane protein expression and simulated integration efficiency
Stephen S Marshall, Michiel JM Niesen, Axel Müller, Katrin Tiemann, Shyam M Saladi, Rachel P Galimidi, Bin Zhang, William M Clemons Jr, Thomas F Miller III
Cell Rep, 16, 2169 (2016)

Exploring the free energy landscape of nucleosomes
Bin Zhang, Weihua Zheng, Garegin A Papoian, Peter G Wolynes
JACS, 138, 8126 (2016)

Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome
Bin Zhang, Peter G Wolynes
PRL, 116, 248101 (2016)

Regulation of multispanning membrane protein topology via post-translational annealing
Reid C Van Lehn, Bin Zhang, Thomas F Miller
Elife, 4, (2015)

Topology, structures, and energy landscapes of human chromosomes
Bin Zhang, Peter G Wolynes
PNAS, 112, 6062, (2015)

Stem cell differentiation as a many-body problem
Bin Zhang, Peter G Wolynes
PNAS, 111, 10185, (2014)

Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation
Bin Zhang, Thomas F Miller
Cell Rep, 2, 924, (2012)

Direct simulation of early-stage Sec-facilitated protein translocation
Bin Zhang, Thomas F Miller
JACS, 134, 13700 (2012)

Hydrophobically stabilized open state for the lateral gate of the Sec translocon
Bin Zhang, Thomas F Miller
PNAS, 107, 5399 (2010)