Bin Zhang

ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 55

Top Venues

bioRxiv : the preprint server for biology

eLife

PLoS computational biology

ACS central science

Massachusetts Institute of Technology

California Institute of Technology (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Massachusetts Institute of Technology Jul 01 2016

United States

Assistant Professor :: Chemistry

Education History

California Institute of Technology Sep 01 2007

United States

PHD :: Chemistry

Publications

Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Bin Zhang, Cong Wang, Henry R Kilgore, Andrew P Latham
Non-specific yet selective interactions contribute to small molecule condensate partitioning behavior. Research square (2024)
Zhuohan Lao, Kartik D Kamat, Zhongling Jiang, Bin Zhang
OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 13 (2024)
Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Cong Wang, Henry R Kilgore, Andrew P Latham, Bin Zhang
Non-specific yet selective interactions contribute to small molecule condensate partitioning behavior. Research square (2024)
Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Zhuohan Lao, Kartik D Kamat, Zhongling Jiang, Bin Zhang
OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 13 (2024)
Xingcheng Lin, Bin Zhang
Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 12 (2024)
Justin Airas, Xinqiang Ding, Bin Zhang
Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks. ACS central science 9 (12) (2023)
Shuming Liu, Cong Wang, Andrew Latham, Xinqiang Ding, Bin Zhang
OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. bioRxiv : the preprint server for biology (2023)
Shuming Liu, Cong Wang, Andrew Latham, Xinqiang Ding, Bin Zhang
OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. bioRxiv : the preprint server for biology (2023)
Justin Airas, Xinqiang Ding, Bin Zhang
Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks. ACS central science 9 (12) (2023)
Songtao Ye, Andrew P Latham, Yuqi Tang, Chia-Heng Hsiung, Junlin Chen, Feng Luo, Liu Yu, Bin Zhang, Zhang Xin
Micropolarity governs the structural organization of biomolecular condensates. Nature chemical biology (2023)
Shuming Liu, Cong Wang, Andrew P Latham, Xinqiang Ding, Bin Zhang
OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates. PLoS computational biology 19 (9) (2023)
Justin Airas, Xinqiang Ding, Bin Zhang
Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks. ACS central science 9 (12) (2023)
Justin Airas, Xinqiang Ding, Bin Zhang
Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks. ACS central science 9 (12) (2023)
Andrew P Latham, Longchen Zhu, Dina A Sharon, Songtao Ye, Adam P Willard, Xin Zhang, Bin Zhang
Frustrated Microphase Separation Produces Interfacial Environment within Biological Condensates. bioRxiv : the preprint server for biology (2023)
Sangwoo Park, Advait Athreya, Gustavo Ezequiel Carrizo, Nils A Benning, Michelle M Mitchener, Natarajan V Bhanu, Benjamin A Garcia, Bin Zhang, Tom W Muir, Erika L Pearce, Taekjip Ha
Electrostatic encoding of genome organization principles within single native nucleosomes. bioRxiv : the preprint server for biology (2023)
Songtao Ye, Andrew P Latham, Yuqi Tang, Chia-Heng Hsiung, Junlin Chen, Feng Luo, Yu Liu, Bin Zhang, Zhang Xin
Micropolarity governs the structural organization of biomolecular condensates. bioRxiv : the preprint server for biology (2023)
Amogh Sood, Bin Zhang
Preserving condensate structure and composition by lowering sequence complexity. bioRxiv : the preprint server for biology (2023)
Sangwoo Park, Advait Athreya, Gustavo Ezequiel Carrizo, Nils A Benning, Michelle M Mitchener, Natarajan V Bhanu, Benjamin A Garcia, Bin Zhang, Tom W Muir, Erika L Pearce, Taekjip Ha
Electrostatic encoding of genome organization principles within single native nucleosomes. bioRxiv : the preprint server for biology (2023)
Zhuohan Lao, Kartik Kamat, Zhongling Jiang, Bin Zhang
OpenNucleome for high resolution nuclear structural and dynamical modeling. bioRxiv : the preprint server for biology (2023)
Justin Airas, Xinqiang Ding, Bin Zhang
Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks. bioRxiv : the preprint server for biology (2023)
Greg Schuette, Xinqiang Ding, Bin Zhang
Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction. bioRxiv : the preprint server for biology (2023)
Sangwoo Park, Advait Athreya, Gustavo Ezequiel Carrizo, Nils A Benning, Michelle M Mitchener, Natarajan V Bhanu, Benjamin A Garcia, Bin Zhang, Tom W Muir, Erika L Pearce, Taekjip Ha
Electrostatic encoding of genome organization principles within single native nucleosomes. bioRxiv : the preprint server for biology (2023)
Xingcheng Lin, Bin Zhang
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization. bioRxiv : the preprint server for biology (2023)
Shuming Liu, Cong Wang, Andrew Latham, Xinqiang Ding, Bin Zhang
OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. bioRxiv : the preprint server for biology (2023)
Rachel Leicher, Adewola Osunsade, Gabriella N L Chua, Sarah C Faulkner, Andrew P Latham, John W Watters, Tuan Nguyen, Emily C Beckwitt, Sophia Christodoulou-Rubalcava, Paul G Young, Bin Zhang, Yael David, Shixin Liu
Single-stranded nucleic acid binding and coacervation by linker histone H1. Nature structural & molecular biology 29 (5) (2022)
Shwetha Srinivasan, Raju Regmi, Xingcheng Lin, Courtney A Dreyer, Xuyan Chen, Steven D Quinn, Wei He, Matthew A Coleman, Kermit L Carraway, Bin Zhang, Gabriela S Schlau-Cohen
Ligand-induced transmembrane conformational coupling in monomeric EGFR. Nature communications 13 (1) (2022)
Shuming Liu, Xingcheng Lin, Bin Zhang
Chromatin fiber breaks into clutches under tension and crowding. Nucleic acids research 50 (17) (2022)
Zhongling Jiang, Yifeng Qi, Kartik Kamat, Bin Zhang
Phase Separation and Correlated Motions in Motorized Genome. The journal of physical chemistry. B 126 (30) (2022)
Liangqi Xie, Peng Dong, Yifeng Qi, Tsung-Han S Hsieh, Brian P English, SeolKyoung Jung, Xingqi Chen, Margherita De Marzio, Rafael Casellas, Howard Y Chang, Bin Zhang, Robert Tse Nan Tjian, Zhe J Liu
BRD2 compartmentalizes the accessible genome. Nature genetics 54 (4) (2022)
Xinqiang Ding, Bin Zhang
Contrastive Learning of Coarse-Grained Force Fields. Journal of chemical theory and computation 18 (10) (2022)
Xingcheng Lin, Yifeng Qi, Andrew P Latham, Bin Zhang
Multiscale modeling of genome organization with maximum entropy optimization. The Journal of chemical physics 155 (1) (2021)
Xingcheng Lin, Rachel Leicher, Shixin Liu, Bin Zhang
Cooperative DNA looping by PRC2 complexes. Nucleic acids research 49 (11) (2021)
Xinqiang Ding, Bin Zhang
DeepBAR: A Fast and Exact Method for Binding Free Energy Computation. The journal of physical chemistry letters 12 (10) (2021)
Yifeng Qi, Bin Zhang
Chromatin network retards nucleoli coalescence. Nature communications 12 (1) (2021)
Andrew P Latham, Bin Zhang
Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation. Journal of chemical theory and computation 17 (5) (2021)
Xinqiang Ding, Xingcheng Lin, Bin Zhang
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface. Nature communications 12 (1) (2021)
Zhongling Jiang, Bin Zhang
On the role of transcription in positioning nucleosomes. PLoS computational biology 17 (1) (2021)
Raju Regmi, Shwetha Srinivasan, Andrew P Latham, Vandna Kukshal, Weidong Cui, Bin Zhang, Ron Bose, Gabriela S Schlau-Cohen
Phosphorylation-Dependent Conformations of the Disordered Carboxyl-Terminus Domain in the Epidermal Growth Factor Receptor. The journal of physical chemistry letters 11 (23) (2020)
Wen Jun Xie, Yifeng Qi, Bin Zhang
Characterizing chromatin folding coordinate and landscape with deep learning. PLoS computational biology 16 (9) (2020)
Xinqiang Ding, Bin Zhang
Computing Absolute Free Energy with Deep Generative Models. The journal of physical chemistry. B 124 (45) (2020)
Liangqi Xie, Peng Dong, Xingqi Chen, Tsung-Han S Hsieh, Sambashiva Banala, Margherita De Marzio, Brian P English, Yifeng Qi, Seol Kyoung Jung, Kyong-Rim Kieffer-Kwon, Wesley R Legant, Anders S Hansen, Anton Schulmann, Rafael Casellas, Bin Zhang, Eric Betzig, Luke D Lavis, Howard Y Chang, Robert Tse Nan Tjian, Zhe J Liu
3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature methods 17 (4) (2020)
Henry R Kilgore, Andrew P Latham, Valerie T Ressler, Bin Zhang, Ronald T Raines
Structure and Dynamics of N-Glycosylated Human Ribonuclease 1. Biochemistry 59 (34) (2020)
Rachel Leicher, Eva J Ge, Xingcheng Lin, Matthew J Reynolds, Wen Jun Xie, Thomas Walz, Bin Zhang, Tom W Muir, Shixin Liu
Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. Proceedings of the National Academy of Sciences of the United States of America 117 (48) (2020)
Andrew P Latham, Bin Zhang
Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins. Journal of chemical theory and computation 16 (1) (2019)
Yifeng Qi, Bin Zhang
Predicting three-dimensional genome organization with chromatin states. PLoS computational biology 15 (6) (2019)
Thomas Parsons, Bin Zhang
Critical role of histone tail entropy in nucleosome unwinding. The Journal of chemical physics 150 (18) (2019)
Jorge L Rosa-Raíces, Bin Zhang, Thomas F Miller Iii
Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals. The Journal of chemical physics 151 (16) (2019)
Andrew P Latham, Bin Zhang
Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data. The journal of physical chemistry. B 123 (5) (2019)

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Publication Activity (10 Years)

Top Topics

Top Venues

Bin Zhang