R. Shen

Structural Insights into the Roles of PARP4 and NAD+ in the Human Vault Cage

This study determines the structure of the human vault cage with PARP4 and NAD+, revealing binding interfaces and NAD+ pockets, and shows proteomics differences in PARP4-depleted vaults.

IOBR2: Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research

IOBR2 is a tool for analyzing tumor microenvironment using multi-omics data, offering modules for preprocessing, estimation, interaction analysis, and visualization.

Structural Basis of Voltage-Dependent Gating in BK Channels and Its Coupling to the Calcium Sensor

This study uses cryo-EM to examine BK channel structures with locked voltage sensor states, revealing how voltage and calcium binding interact to control channel gating.

Physical structure and interstitial flows govern microbial life in microenvironments

The paper quantifies how microscale pore structures and interstitial flows affect nutrient supply and microbial function in microenvironments using experiments and simulations.

Adaptation of a Mutual Exclusivity Framework to Identify Driver Mutations within Biological Pathways

The paper introduces MAGPIE, a computational method to identify driver mutations in cancer pathways by analyzing mutual exclusivity patterns, and validates it on melanoma data.

Forsythoside A blocks the infection of Avian Infectious Bronchitis Virus through binding S1 subunit

This study shows Forsythoside A inhibits Avian Infectious Bronchitis Virus by binding to its S1 subunit, preventing viral attachment and infection.

Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits

The paper identifies and validates a six-gene regulatory circuit upstream of NLP6/7 in Arabidopsis and tomato, revealing conservation and divergence in nitrogen-responsive gene regulation across species.

Formate Promotes Invasion and Metastasis by Activating Fatty Acid Synthesis and Matrix Metalloproteinases

Dynamics of activation in the voltage-sensing domain of Ci-VSP

This study uses molecular dynamics simulations and computational frameworks to elucidate the microscopic mechanism of voltage-sensing domain activation in Ci-VSP.

State Dependent Anionic Pore Currents Conducted by Single Countercharge Mutants in a Voltage-Sensing Phosphatase

The paper shows that mutating a countercharge residue in a voltage-sensing phosphatase creates anion-selective omega currents through altered electrostatic potential and water pathways.

Mechanism of Voltage Gating in the Voltage-Sensing Phosphatase Ci-VSP

The paper investigates the voltage gating mechanism of Ci-VSP's voltage-sensing domain using simulations and experiments, identifying four states and charge movement during activation.

Harbingers of Aggressive Prostate Cancer: Precision Oncology Case Studies

This study identifies molecular features of primary prostate cancer and their relation to metastasis using genomic and histopathological analysis.

Molecular Modeling Evaluation of the Binding Effect of Ritonavir, Lopinavir and Darunavir to Severe Acute Respiratory Syndrome Coronavirus 2 Proteases

This study evaluates the binding of ritonavir, lopinavir, and darunavir to SARS-CoV-2 proteases using molecular modeling, finding that ritonavir and lopinavir inhibit CEP_C30 more effectively than darunavir inhibits PLVP.