Bin Zhang

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 66 papers. Top paper: “Spatially clustered type I interferon responses at injury borderzones”.

Spatially clustered type I interferon responses at injury borderzones

Nature(2024)10.1038/s41586-024-07806-1

N/A

1.3DataRank · unranked

62 citations

David Calcagno, Justin Yu, Bin Zhang, N. Taghdiri, R. Sehgal +13 more

Ligand-induced transmembrane conformational coupling in monomeric EGFR

Nature Communications(2022)10.1038/s41467-022-31299-z

N/A

0.524DataRank · unranked

32 citations

Raju Regmi, Xingcheng Lin, Courtney A. Dreyer, Xuyan Chen, Steven D. Quinn +6 more

Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction

Biophysical Journal(2023)10.1016/j.bpj.2023.07.017

N/A

0.396DataRank · unranked

13 citations

Xinqiang Ding, Bin Zhang, Greg Schuette

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.27.968735

N/A

0.360DataRank · unranked

10 citations

Alejandro Reyes, Sarah E. Johnstone, Martin J. Aryee, B Bernstein, Bin Zhang +1 more

Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.08.556923

N/A

0.165DataRank · unranked

2 citations

Xinqiang Ding, Bin Zhang, Justin Airas

Microphase separation produces interfacial environment within diblock biomolecular condensates

eLife(2025)10.7554/elife.90750.4

N/A

0.165DataRank · unranked

2 citations

Longchen Zhu, Dina A. Sharon, Songtao Ye, Adam P. Willard, Xin Zhang +2 more

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

Nature Communications(2021)10.1038/s41467-021-21377-z

N/A

0DataRank · unranked

72 citations

Xingcheng Lin, Bin Zhang, Xinqiang Ding

Unifying coarse-grained force fields for folded and disordered proteins

Current Opinion in Structural Biology(2021)10.1016/j.sbi.2021.08.006

N/A

0DataRank · unranked

50 citations

Bin Zhang, Andrew P. Latham

Cooperative DNA looping by PRC2 complexes

Nucleic Acids Research(2021)10.1093/nar/gkab441

N/A

0DataRank · unranked

43 citations

Rachel Leicher, Shixin Liu, Bin Zhang, Xingcheng Lin

On the role of transcription in positioning nucleosomes

PLoS Computational Biology(2021)10.1371/journal.pcbi.1008556

N/A

0DataRank · unranked

19 citations

Bin Zhang, Zhongling Jiang

Quantifying the Stability of Coupled Genetic and Epigenetic Switches With Variational Methods

Frontiers in Genetics(2021)10.3389/fgene.2020.636724

N/A

0DataRank · unranked

6 citations

Bin Zhang, Amogh Sood

Genome Compartmentalization with Nuclear Landmarks: Random yet Precise

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.12.468401

N/A

0DataRank · unranked

8 citations

Yifeng Qi, Yuchuan Wang, Jian Ma, Bin Zhang, Kartik Kamat

Chromatin Network Retards Droplet Coalescence

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.02.433564

N/A

0DataRank · unranked

7 citations

Bin Zhang, Yifeng Qi

Single-stranded nucleic acid sensing and coacervation by linker histone H1

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.17.435841

N/A

0DataRank · unranked

6 citations

Adewola Osunsade, Andrew P. Latham, Gabriella N. L. Chua, John W. Watters, Sophia Christodoulou-Rubalcava +4 more

Consistent Force Field Captures Homolog Resolved HP1 Phase Separation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.06.425600

N/A

0DataRank · unranked

4 citations

Bin Zhang, Andrew P. Latham

Chromatin fiber breaks into clutches under tension and crowding

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.16.468645

N/A

0DataRank · unranked

3 citations

Xingcheng Lin, Bin Zhang, Shuming Liu

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.06.425601

N/A

0DataRank · unranked

2 citations

Xingcheng Lin, Bin Zhang, Xinqiang Ding

On the stability and layered organization of protein-DNA condensates

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.22.457249

N/A

0DataRank · unranked

2 citations

Bin Zhang, Andrew P. Latham

Ligand-induced transmembrane conformational coupling in monomeric EGFR

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.28.466294

N/A

0DataRank · unranked

1 citations

Raju Regmi, Xingcheng Lin, Courtney A. Dreyer, Xuyan Chen, Steven D. Quinn +6 more

On the stability and layered organization of protein-DNA condensates

Biophysical Journal(2022)10.1016/j.bpj.2022.03.028

N/A

0DataRank · unranked

59 citations

Bin Zhang, Andrew P. Latham

Molecular determinants for the layering and coarsening of biological condensates

Aggregate(2022)10.1002/agt2.306

N/A

0DataRank · unranked

33 citations

Bin Zhang, Andrew P. Latham

3DGenBench: a web-server to benchmark computational models for 3D Genomics

Nucleic Acids Research(2022)10.1093/nar/gkac396

N/A

0DataRank · unranked

19 citations

Emil Viesná, Mateusz Chiliński, Yifeng Qi, Hossein Salari, Marco Di Stefano +9 more

Phase Separation and Correlated Motions in Motorized Genome

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.10.491350

N/A

0DataRank · unranked

0 citations

Yifeng Qi, Kartik Kamat, Bin Zhang, Zhongling Jiang

Micropolarity governs the structural organization of biomolecular condensates

Nature Chemical Biology(2023)10.1038/s41589-023-01477-1

N/A

0DataRank · unranked

123 citations

Andrew P. Latham, Yuqi Tang, Chia‐Heng Hsiung, Junlin Chen, Feng Luo +4 more

OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates

PLoS Computational Biology(2023)10.1371/journal.pcbi.1011442

N/A

0DataRank · unranked

39 citations

Cong Wang, Andrew P. Latham, Xinqiang Ding, Bin Zhang, Shuming Liu

Explicit ion modeling predicts physicochemical interactions for chromatin organization

eLife(2023)10.7554/elife.90073

N/A

0DataRank · unranked

33 citations

Bin Zhang, Xingcheng Lin

Compartmentalization with nuclear landmarks yields random, yet precise, genome organization

Biophysical Journal(2023)10.1016/j.bpj.2023.03.003

N/A

0DataRank · unranked

38 citations

Zhuohan Lao, Yifeng Qi, Yuchuan Wang, Jian Ma, Bin Zhang +1 more

Micropolarity governs the structural organization of biomolecular condensates

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.30.534881

N/A

0DataRank · unranked

20 citations

Andrew P. Latham, Yuqi Tang, Chia‐Heng Hsiung, Junlin Chen, Feng Luo +4 more

Microphase separation produces interfacial environment within diblock biomolecular condensates

eLife(2023)10.7554/elife.90750

N/A

0DataRank · unranked

17 citations

Longchen Zhu, Dina A. Sharon, Songtao Ye, Adam P. Willard, Xin Zhang +2 more

Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.30.534967

N/A

0DataRank · unranked

9 citations

Longchen Zhu, Dina A. Sharon, Songtao Ye, Adam P. Willard, Xin Zhang +2 more

Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.17.533194

N/A

0DataRank · unranked

8 citations

Xinqiang Ding, Bin Zhang, Greg Schuette

Electrostatic encoding of genome organization principles within single native nucleosomes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.08.570828

N/A

0DataRank · unranked

7 citations

Advait Athreya, Gustavo Carrizo, Nils A. Benning, Michelle M. Mitchener, Natarajan V. Bhanu +6 more

OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.19.537533

N/A

0DataRank · unranked

3 citations

Cong Wang, Andrew P. Latham, Xinqiang Ding, Bin Zhang, Shuming Liu

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.16.541030

N/A

0DataRank · unranked

3 citations

Bin Zhang, Xingcheng Lin

OpenNucleome for high resolution nuclear structural and dynamical modeling

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.16.562451

N/A

0DataRank · unranked

1 citations

Kartik Kamat, Zhongling Jiang, Bin Zhang, Zhuohan Lao

Reviewer #2 (Public Review): Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

(2023)10.7554/elife.90073.1.sa0

N/A

0DataRank · unranked

0 citations

Bin Zhang, Lin Xingcheng

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

(2023)10.7554/elife.90073.1

N/A

0DataRank · unranked

0 citations

Bin Zhang, Xingcheng Lin

Reviewer #1 (Public Review): Frustrated Microphase Separation Produces Interfacial Environment within Biological Condensates

(2023)10.7554/elife.90750.1.sa1

N/A

0DataRank · unranked

0 citations

Longchen Zhu, Dina A. Sharon, Songtao Ye, Adam P. Willard, Xin Zhang +2 more

Preserving condensate structure and composition by lowering sequence complexity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.29.569249

N/A

0DataRank · unranked

0 citations

Bin Zhang, Amogh Sood

From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization

Annual Review of Biophysics(2024)10.1146/annurev-biophys-030822-032650

N/A

0DataRank · unranked

39 citations

Advait Athreya, Zhuohan Lao, Bin Zhang, Shuming Liu

Nonspecific Yet Selective Interactions Contribute to Small Molecule Condensate Binding

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c01024

N/A

0DataRank · unranked

14 citations

Henry R. Kilgore, Andrew P. Latham, Bin Zhang, Cong Wang

Preserving condensate structure and composition by lowering sequence complexity

Biophysical Journal(2024)10.1016/j.bpj.2024.05.026

N/A

0DataRank · unranked

10 citations

Bin Zhang, Amogh Sood

OpenNucleome for high-resolution nuclear structural and dynamical modeling

eLife(2024)10.7554/elife.93223

N/A

0DataRank · unranked

4 citations

Kartik Kamat, Zhongling Jiang, Bin Zhang, Zhuohan Lao

Dynamical phase transition in models that couple chromatin folding with histone modifications

Physical review. E(2024)10.1103/physreve.109.054411

N/A

0DataRank · unranked

4 citations

Greg Schuette, Bin Zhang, Amogh Sood

OpenNucleome for high resolution nuclear structural and dynamical modeling

eLife(2024)10.7554/elife.93223.1

N/A

0DataRank · unranked

2 citations

Kartik Kamat, Zhongling Jiang, Bin Zhang, Zhuohan Lao

Non-specific yet selective interactions contribute to small molecule condensate partitioning behavior

Research Square(2024)10.21203/rs.3.rs-4784242/v1

N/A

0DataRank · unranked

1 citations

Cong Wang, Henry R. Kilgore, Andrew P. Latham, Bin Zhang

Author Response: Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

(2024)10.7554/elife.90073.2.sa2

N/A

0DataRank · unranked

0 citations

Bin Zhang, Xingcheng Lin

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

eLife(2024)10.7554/elife.90073.2

N/A

0DataRank · unranked

0 citations

Bin Zhang, Xingcheng Lin

Reviewer #1 (Public Review): OpenNucleome for high resolution nuclear structural and dynamical modeling

(2024)10.7554/elife.93223.1.sa2

N/A

0DataRank · unranked

0 citations

Kartik Kamat, Zhongling Jiang, Bin Zhang, Zhuohan Lao

Author response: Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates

(2024)10.7554/elife.90750.2.sa7

N/A

0DataRank · unranked

0 citations

Longchen Zhu, Dina A. Sharon, Songtao Ye, Adam P. Willard, Xin Zhang +2 more

Reviewer #1 (Public Review): Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates

(2024)10.7554/elife.90750.3.sa1

N/A

0DataRank · unranked

0 citations

Longchen Zhu, Dina A. Sharon, Songtao Ye, Adam P. Willard, Xin Zhang +2 more

ChromoGen: Diffusion model predicts single-cell chromatin conformations

Research Square(2024)10.21203/rs.3.rs-4630850/v1

N/A

0DataRank · unranked

0 citations

Greg Schuette, Zhuohan Lao, Bin Zhang

Scaling Graph Neural Networks to Large Proteins

arXiv (Cornell University)(2024)10.48550/arxiv.2410.03921

N/A

0DataRank · unranked

0 citations

Bin Zhang, Justin Airas

ChromoGen: Diffusion model predicts single-cell chromatin conformations

Science Advances(2025)10.1126/sciadv.adr8265

N/A

0DataRank · unranked

23 citations

Zhuohan Lao, Bin Zhang, Greg Schuette

Scaling Graph Neural Networks to Large Proteins

Journal of Chemical Theory and Computation(2025)10.1021/acs.jctc.4c01420

N/A

0DataRank · unranked

6 citations

Bin Zhang, Justin Airas

Toward decoding the mechanisms that shape sub-megabase-scale genome organization

Current Opinion in Structural Biology(2025)10.1016/j.sbi.2025.103062

N/A

0DataRank · unranked

4 citations

Bin Zhang, Joseph M. Paggi

Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

Biophysical Journal(2025)10.1016/j.bpj.2025.11.2686

N/A

0DataRank · unranked

4 citations

Shuming Liu, Xingcheng Lin, Ilona Christy Unarta, Xuhui Huang, Bin Zhang +1 more

Euchromatin forms condensed domains with short active regions on the surface

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.05.668703

N/A

0DataRank · unranked

8 citations

Bin Zhang, Joseph M. Paggi

Active regulation of the epidermal growth factor receptor by the membrane bilayer

eLife(2025)10.7554/elife.108789

N/A

0DataRank · unranked

3 citations

Xingcheng Lin, Xuyan Chen, Raju Regmi, Bin Zhang, Gabriela S. Schlau‐Cohen +1 more

Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2003395117

N/A

0DataRank · unranked

65 citations

Eva J. Ge, Xingcheng Lin, Matthew J. Reynolds, Wen Jun Xie, Thomas Walz +4 more

Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.06.668966

N/A

0DataRank · unranked

1 citations

Bin Zhang, Cong Wang

Structure and Dynamics of N-Glycosylated Human Ribonuclease 1

Biochemistry(2020)10.1021/acs.biochem.0c00191

N/A

0DataRank · unranked

13 citations

Andrew P. Latham, Valerie T. Ressler, Bin Zhang, Ronald T. Raines, Henry R. Kilgore

Quantifying epigenetic stability with minimum action paths

Physical review. E(2020)10.1103/physreve.101.062409

N/A

0DataRank · unranked

12 citations

Bin Zhang, Amogh Sood

Characterizing chromatin folding coordinate and landscape with deep learning

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008262

N/A

0DataRank · unranked

28 citations

Yifeng Qi, Bin Zhang, Wen Jun Xie

On the role of transcription in positioning nucleosomes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.07.029892

N/A

0DataRank · unranked

1 citations

Bin Zhang, Zhongling Jiang

Chromatin network retards nucleoli coalescence

Nature Communications(2021)10.1038/s41467-021-27123-9

N/A

0DataRank · unranked

75 citations

Bin Zhang, Yifeng Qi