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)

Data-driven polymer model for mechanistic exploration of diploid genome organization

We introduce a polymer model to study the organization of the diploid human genome. It is data-driven as all parameters can be derived from Hi-C data; it is also a mechanistic model since the energy function is explicitly written out based on a few biologically motivated hypotheses. These two features distinguish the model from existing approaches and make it useful both for reconstructing genome structures and for exploring the principles of genome organization.

Yifeng Qi, Alejandro Reyes, Sarah E Johnstone, Martin J Aryee, Bradley E Bernstein, Bin Zhang

Biophys J, in press

 

Full List

* indicates co-corresponding authors.

Submitted

Multiscale Modeling of Genome Organization with Maximum Entropy Optimization
Xingcheng Lin, Yifeng Qi, Andrew Latham, Bin Zhang

DeepBAR: A Fast and Exact Method for Binding Free Energy Computation
Xinqiang Ding, Bin Zhang

Cooperative DNA Looping by PRC2 Complexes via Allosteric Communication
Xingcheng Lin, Rachel Leicher, Shixin Liu, Bin Zhang

Consistent Force Field Captures Homolog Resolved HP1 Phase Separation
Andrew P. Latham, Bin Zhang

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*

2021

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

2020

Quantifying the stability of coupled genetic and epigenetic switch with variational methods
Amogh Sood, Bin Zhang
Frontiers in Genetics, 11 (2021)

On the role of transcription in positioning nucleosomes
Zhongling Jiang, Bin Zhang
PLoS Comp Bio, in press

Phosphorylation-Dependent Conformations of the Disordered Carboxyl-Terminus Domain in the Epidermal Growth Factor Receptor
Raju Regmi, Shwetha Srinivasan, Vandna Kukshal, Andrew P. Latham, Weidong Cui, Bin Zhang, Ron Bose, Gabriela S. Schlau-Cohen
J Phy Chem Lett, 11:10037-10044 (2020)

Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin
Rachel Leicher, J Ge Eva, Xingcheng Lin, Matthew J Reynolds, Thomas Walz, Bin Zhang*, Tom W Muir, Shixin Liu*
PNAS, 117:30465-30475 (2020)

Computing Absolute Free Energy with Deep Generative Models
Xinqiang Ding, Bin Zhang
J Phys Chem B, 124:10166–10172 (2020)

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
Biophys J, 119:1905-1916 (2020) Highlighted as New and Notable

Characterizing chromatin folding coordinate and landscape with deep learning
Wen Jun Xie, Yifeng Qi, Bin Zhang
PLoS Comp Bio, 16, e1008262 (2020)

Structural and Dynamic Features of N-glycosylated Human RNase1
Henry Kilgore, Andrew Latham, Valerie Ressler, Bin Zhang*, Ronald T. Raines*
Biochemistry, 59:3148–3156 (2020)

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer
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, 182:1474-1489.e23 (2020)

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) Highlighted as Editors’ Choice

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)