Publications by authors named "She Zhang"

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Advances in tuberculosis co-infections: Mechanisms, diagnosis, and therapeutics.
Shixiong He, Changjiao Luan, Jiaqi Gao, Feng Lu, Fang Tian, She Zhang

Microb Pathog· January 2026

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Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRAS .
Neha Vithani, She Zhang, Jeffrey P Thompson, Lara A Patel, Alex Demidov

J Chem Inf Model· November 2024

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Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.
Anupam Banerjee, She Zhang, Ivet Bahar

Brief Funct Genomics· September 2024

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Disulfidptosis-related gene predicts prognosis and indicates tumor immune infiltration in lung adenocarcinoma.
Jing Zhu, Hui Ge, Yinsong Chen, She Zhang, Junjie Wu

Transl Cancer Res· September 2024

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A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].
Anthony T Bogetti, Jeremy M G Leung, John D Russo, She Zhang, Jeff P Thompson

Living J Comput Mol Sci· January 2023

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Swollen inguinal lymph nodes with low fever and night sweat: diagnosis and treatment of case of cat-scratch disease lymphadenitis with sinus formation.
Miao Zhu, She Zhang, Qingqing Shi, Xing Sun, Xiaowei Zhang

Heliyon· September 2022

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Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow.
Omer Acar, She Zhang, Ivet Bahar, Anne-Ruxandra Carvunis

PLoS Comput Biol· May 2022

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Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories.
She Zhang, Jeff P Thompson, Junchao Xia, Anthony T Bogetti, Forrest York

J Chem Inf Model· April 2022

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WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.
John D Russo, She Zhang, Jeremy M G Leung, Anthony T Bogetti, Jeff P Thompson

J Chem Theory Comput· February 2022

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ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution.
Burak T Kaynak, She Zhang, Ivet Bahar, Pemra Doruker

Bioinformatics· November 2021

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ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.
She Zhang, James M Krieger, Yan Zhang, Cihan Kaya, Burak Kaynak

Bioinformatics· October 2021

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Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.
Yan Zhang, She Zhang, Jianhua Xing, Ivet Bahar

J Chem Phys· May 2021

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HiDeF: identifying persistent structures in multiscale 'omics data.
Fan Zheng, She Zhang, Christopher Churas, Dexter Pratt, Ivet Bahar

Genome Biol· January 2021

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Identifying persistent structures in multiscale 'omics data.
Fan Zheng, She Zhang, Christopher Churas, Dexter Pratt, Ivet Bahar

bioRxiv· October 2020

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Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation.
Mary Hongying Cheng, She Zhang, Rebecca A Porritt, Magali Noval Rivas, Lisa Paschold

Proc Natl Acad Sci U S A· October 2020

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Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.
Yan Zhang, Pemra Doruker, Burak Kaynak, She Zhang, James Krieger

Curr Opin Struct Biol· June 2020

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An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations.
Mary Hongying Cheng, She Zhang, Rebecca A Porritt, Moshe Arditi, Ivet Bahar

bioRxiv· May 2020

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Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation.
She Zhang, Fangyuan Chen, Ivet Bahar

Nucleic Acids Res· February 2020

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Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations.
Mary Hongying Cheng, Luca Ponzoni, Tatiana Sorkina, Ji Young Lee, She Zhang

Neuropharmacology· December 2019

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Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity.
She Zhang, Hongchun Li, James M Krieger, Ivet Bahar

Mol Biol Evol· September 2019

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Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.
Karolina Mikulska-Ruminska, Indira Shrivastava, James Krieger, She Zhang, Hongchun Li

J Chem Inf Model· May 2019

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Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization.
Luca Ponzoni, She Zhang, Mary Hongying Cheng, Ivet Bahar

Philos Trans R Soc Lond B Biol Sci· June 2018

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Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar

Nucleic Acids Res· April 2017

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Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions.
Ivet Bahar, Mary Hongying Cheng, Ji Young Lee, Cihan Kaya, She Zhang

Biophys J· September 2015

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Curcumin modulates cannabinoid receptors in liver fibrosis in vivo and inhibits extracellular matrix expression in hepatic stellate cells by suppressing cannabinoid receptor type-1 in vitro.
Zili Zhang, Yao Guo, She Zhang, Yan Zhang, Yuqing Wang

Eur J Pharmacol· December 2013

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