Yihan Shao

Also affiliated with Brandeis University, University of Oklahoma

Physics and AstronomyBiochemistry, Genetics and Molecular BiologyMaterials ScienceChemistry

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 59 papers. Top paper: “Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions”.

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00565

N/A

0.710DataRank · unranked

113 citations

Junjie Yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang +5 more

In vivo three-dimensional brain imaging with chemiluminescence probes in Alzheimer’s disease models

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2310131120

N/A

0.533DataRank · unranked

34 citations

Carly Wickizer, Weihua Ding, Richard Van, Liuyue Yang, Biyue Zhu +10 more

Cavity quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis. II. Analytic energy gradient

The Journal of Chemical Physics(2022)10.1063/5.0082386

N/A

0.520DataRank · unranked

31 citations

Zheng Pei, Erick Calderon Leon, Carly Wickizer, Binbin Weng, Yuezhi Mao +3 more

Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian

The Journal of Physical Chemistry B(2022)10.1021/acs.jpcb.2c02262

N/A

0.464DataRank · unranked

21 citations

Richard Van, Evgeny Epifanovsky, Jian Liu, Jingzhi Pu, Kwangho Nam +2 more

Development of a highly-specific 18F-labeled irreversible positron emission tomography tracer for monoacylglycerol lipase mapping

Acta Pharmaceutica Sinica B(2021)10.1016/j.apsb.2021.01.021

N/A

0.425DataRank · unranked

16 citations

Wakana Mori, Jian Rong, Michael A. Schafroth, Tuo Shao, Richard Van +17 more

Epitope alteration by small molecules and applications in drug discovery

Chemical Science(2022)10.1039/d2sc02819k

N/A

0.345DataRank · unranked

9 citations

Jing Yang, Richard Van, Fan Yang, Yue Yu, Astra Yu +16 more

Development of a triazolobenzodiazepine-based PET probe for subtype-selective vasopressin 1A receptor imaging

Pharmacological Research(2021)10.1016/j.phrs.2021.105886

N/A

0.312DataRank · unranked

7 citations

Zhiwei Xiao, Xiaotian Xia, Jiahui Chen, Richard Van, Shi Kuang +10 more

Synthesis and preliminary evaluation of 4-hydroxy-6-(3-[11C]methoxyphenethyl)pyridazin-3(2H)-one, a 11C-labeled -amino acid oxidase (DAAO) inhibitor for PET imaging

Bioorganic & Medicinal Chemistry Letters(2020)10.1016/j.bmcl.2020.127326

N/A

0.269DataRank · unranked

5 citations

Yiding Zhang, Zhen Chen, Katsushi Kumata, Richard Van, Jian Rong +14 more

MetaPhenotype: A Transferable Meta-Learning Model for Single-Cell Mass Spectrometry-Based Cell Phenotype Prediction Using Limited Number of Cells

Analytical Chemistry(2024)10.1021/acs.analchem.4c02038

N/A

0.208DataRank · unranked

3 citations

Tra D. Nguyen, Yunpeng Lan, Wen Yang, Dan Chen, Yihan Shao +2 more

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

ChemRxiv(2020)10.26434/chemrxiv.12675428.v1

N/A

0DataRank · unranked

1 citations

Pengfei Li, Jianing Wang, Yuanfei Xue, Yan Mo, Jun Zheng +4 more

Can We See the Energy Densities? I. Insights from Real-Time Time-Dependent Density Functional Theory Simulations

ChemRxiv(2020)10.26434/chemrxiv.12808415.v1

N/A

0DataRank · unranked

1 citations

Zheng Pei, Jingheng Deng, Qin Wu, Yuezhi Mao, Zhibo Yang +5 more

Can We See the Energy Densities? II. Insights from Linear-Response Time-Dependent Density Functional Theory Calculations

ChemRxiv(2020)10.26434/chemrxiv.12808526.v1

N/A

0DataRank · unranked

0 citations

Junjie Yang, Jingheng Deng, Yuezhi Mao, Qin Wu, Zhibo Yang +5 more

Can We See the Energy Densities? II. Insights from Linear-Response Time-Dependent Density Functional Theory Calculations

ChemRxiv(2020)10.26434/chemrxiv.12808526

N/A

0DataRank · unranked

0 citations

Junjie Yang, Jingheng Deng, Yuezhi Mao, Qin Wu, Zhibo Yang +5 more

Can We See the Energy Densities? I. Insights from Real-Time Time-Dependent Density Functional Theory Simulations

ChemRxiv(2020)10.26434/chemrxiv.12808415

N/A

0DataRank · unranked

0 citations

Zheng Pei, Jingheng Deng, Qin Wu, Yuezhi Mao, Zhibo Yang +5 more

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

ChemRxiv(2020)10.26434/chemrxiv.12675428

N/A

0DataRank · unranked

0 citations

Pengfei Li, Jianing Wang, Yuanfei Xue, Yan Mo, Jun Zheng +4 more

Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference-Potential. 4. Adaptive QM/MM

ChemRxiv(2020)10.26434/chemrxiv.12764726

N/A

0DataRank · unranked

0 citations

Wei Liu, Pengfei Li, Yan Mo, Wenxin Hu, Jun Zheng +4 more

Smart Chemiluminescence Probes and Dual-Amplification of Signal for Detection of Amyloid Beta Species in Alzheimer’s Disease Model

ChemRxiv(2020)10.26434/chemrxiv.12142578

N/A

0DataRank · unranked

0 citations

Wei Yin, Richard Van, Keyi Yin, Peng Wang, Chao Zheng +6 more

Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00245

N/A

0DataRank · unranked

23 citations

Ryan Snyder, Mulpuri Nagaraju, Yan Zhou, Pedro Ojeda-May, Seth Keeton +4 more

Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

ChemRxiv(2021)10.26434/chemrxiv.14745510.v1

N/A

0DataRank · unranked

12 citations

Junjie Yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang +5 more

Development of a Triazolobenzodiazepine-Based PET Probe for Subtype-Selective Vasopressin 1A Receptor Imaging

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.09.430516

N/A

0DataRank · unranked

0 citations

Zhiwei Xiao, Xiaotian Xia, Jiahui Chen, Richard Van, Shi Kuang +10 more

Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential

Figshare(2021)10.33774/chemrxiv-2021-m14db

N/A

0DataRank · unranked

0 citations

Jianing Wang, Wenxin Hu, Jun Zheng, Yongle Li, Xiaoliang Pan +5 more

Cavity quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis. II. Analytic energy gradient

ChemRxiv(2021)10.26434/chemrxiv-2021-lf5m2

N/A

0DataRank · unranked

0 citations

Zheng Pei, Erick Calderon Leon, Carly Wickizer, Binbin Weng, Yuezhi Mao +3 more

Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference-Potential. 4. Adaptive QM/MM

ChemRxiv(2021)10.26434/chemrxiv.12764726.v3

N/A

0DataRank · unranked

0 citations

Wei Liu, Pengfei Li, Yan Mo, Wenxin Hu, Jun Zheng +4 more

Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

ChemRxiv(2021)10.26434/chemrxiv.14745510

N/A

0DataRank · unranked

0 citations

Junjie Yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang +5 more

Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations

Physical Chemistry Chemical Physics(2022)10.1039/d2cp02820d

N/A

0DataRank · unranked

16 citations

Bryant Kim, Xiaoliang Pan, Yihan Shao, Jingzhi Pu, Ryan Snyder

Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semi-empirical QM/MM Hamiltonian

ChemRxiv(2022)10.26434/chemrxiv-2022-0zg7j

N/A

0DataRank · unranked

2 citations

Richard Van, Evgeny Epifanovsky, Jian Liu, Jingzhi Pu, Kwangho Nam +2 more

Analytic High-Order Energy Derivatives for Metal Nanoparticle-Mediated Infrared and Raman Scattering Spectra within the Framework of Quantum Mechanics/Molecular Mechanics Model with Induced Charges and Dipoles

ChemRxiv(2022)10.26434/chemrxiv-2022-dwdp4

N/A

0DataRank · unranked

1 citations

Yuezhi Mao, Yihan Shao, WanZhen Liang, Zheng Pei

Cavity quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis. II. Analytic energy gradient

ChemRxiv(2022)10.26434/chemrxiv-2021-lf5m2-v2

N/A

0DataRank · unranked

0 citations

Zheng Pei, Erick Calderon Leon, Carly Wickizer, Binbin Weng, Yuezhi Mao +3 more

Visualization of Electron Density Changes Along Chemical Reaction Pathways

ChemRxiv(2022)10.26434/chemrxiv-2022-tfqnn

N/A

0DataRank · unranked

0 citations

Vardhan Satalkar, Junjie Yang, Xiaoliang Pan, Zheng Pei, Aayushi Chatterji +6 more

Visualization of electron density changes along chemical reaction pathways

Molecular Physics(2022)10.1080/00268976.2022.2113566

N/A

0DataRank · unranked

0 citations

Vardhan Satalkar, Junjie Yang, Xiaoliang Pan, Zheng Pei, Aayushi Chatterji +6 more

Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations

RSC Advances(2023)10.1039/d2ra08180f

N/A

0DataRank · unranked

31 citations

Richard Van, Xiaoliang Pan, Ji Hwan Park, Yuezhi Mao, Jingzhi Pu +3 more

Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation

The Journal of Chemical Physics(2023)10.1063/5.0156327

N/A

0DataRank · unranked

21 citations

Bryant Kim, Xiaoliang Pan, Yihan Shao, Jingzhi Pu, Ryan Snyder

Influence of structural moieties in squaraine dyes on optoacoustic signal shape and intensity

Chem(2023)10.1016/j.chempr.2023.11.016

N/A

0DataRank · unranked

11 citations

Carly Wickizer, Richard Van, Emmanuel Ramsey Buabeng, Megan R. Lerner, William E. Grizzle +4 more

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00973

N/A

0DataRank · unranked

10 citations

Richard Van, Jingzhi Pu, Kwangho Nam, Yuezhi Mao, Yihan Shao +1 more

Training machine learning potentials for reactive systems: A Colab tutorial on basic models

Journal of Computational Chemistry(2023)10.1002/jcc.27269

N/A

0DataRank · unranked

9 citations

Ryan Snyder, Jianing Wang, Chance Lander, Carly Wickizer, Richard Van +7 more

Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls

The Journal of Physical Chemistry Letters(2023)10.1021/acs.jpclett.3c00671

N/A

0DataRank · unranked

8 citations

Yuanfei Xue, Pengfei Li, Xiaoliang Pan, Meiting Wang, Yihan Shao +3 more

The Training of Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models

ChemRxiv(2023)10.26434/chemrxiv-2023-545gw

N/A

0DataRank · unranked

2 citations

Ryan Snyder, Jianing Wang, Chance Lander, Carly Wickizer, Richard Van +7 more

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

ChemRxiv(2023)10.26434/chemrxiv-2023-mrm25

N/A

0DataRank · unranked

0 citations

Richard Van, Jingzhi Pu, Kwangho Nam, Yuezhi Mao, Yihan Shao +1 more

Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

Biochemistry(2024)10.1021/acs.biochem.4c00651

N/A

0DataRank · unranked

5 citations

Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul K. Agarwal, Bernard R. Brooks +3 more

Imaging poly(ADP-ribose) polymerase-1 (PARP1) in vivo with 18F-labeled brain penetrant positron emission tomography (PET) ligand

ChemRxiv(2024)10.26434/chemrxiv-2024-8pqmg-v2

N/A

0DataRank · unranked

2 citations

Jiahui Chen, Jimmy S. Patel, Wenqing Ran, Yinlong Li, Richard Van +19 more

Exploring CRISPR-Cas9 HNH-Domain Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

ChemRxiv(2024)10.26434/chemrxiv-2024-kpr4t

N/A

0DataRank · unranked

0 citations

Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul K. Agarwal, Bernard R. Brooks +3 more

On the Entanglement of Chromophore and Solvent Orbitals

ChemRxiv(2024)10.26434/chemrxiv-2024-zqbjt

N/A

0DataRank · unranked

0 citations

Zheng Pei, Kim Ngan Huynh, Junjie Yang, Xiaoliang Pan, Binju Wang +3 more

Imaging poly(ADP-ribose) polymerase-1 (PARP1) in vivo with 18F-labeled brain penetrant positron emission tomography (PET) ligand

Acta Pharmaceutica Sinica B(2025)10.1016/j.apsb.2025.05.020

N/A

0DataRank · unranked

13 citations

Jiahui Chen, Jimmy S. Patel, Wenqing Ran, Yinlong Li, Richard Van +19 more

On the entanglement of chromophore and solvent orbitals

The Journal of Chemical Physics(2025)10.1063/5.0242844

N/A

0DataRank · unranked

5 citations

Zheng Pei, Kim Ngan Huynh, Junjie Yang, Xiaoliang Pan, Binju Wang +3 more

Development of a Novel 18F-Labeled Radioligand for Imaging Phosphodiesterase 7 with Positron Emission Tomography

Molecular Pharmaceutics(2025)10.1021/acs.molpharmaceut.4c01379

N/A

0DataRank · unranked

6 citations

Chunyu Zhao, Ahmad Chaudhary, Evan R. Jones, Richard Van, Zhendong Song +15 more

Development of a novel 18F-labeled reversible-binding radioligand for imaging monoacylglycerol lipase with positron emission tomography

Acta Pharmaceutica Sinica B(2025)10.1016/j.apsb.2025.05.041

N/A

0DataRank · unranked

3 citations

Chunyu Zhao, Ahmad Chaudhary, Tim Ware, Richard Van, Yinlong Li +16 more

Detection of misfolded proteins in neurodegenerative disease models with a highly sensitive chemiluminescence probe

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.12.648090

N/A

0DataRank · unranked

0 citations

Richard Van, Huizhe Wang, Shi Kuang, Yuntao Jia, Erick Calderon Leon +13 more

Enhancing Gaussian process regression-accelerated QM/MM free energy simulations using atomic environment descriptors

ChemRxiv(2025)10.26434/chemrxiv-2025-hg8n7

N/A

0DataRank · unranked

0 citations

Dongru Li, T.‐L. HO, Bryant Kim, Hysum Qazi, Xiaoliang Pan +3 more

Enhancing Gaussian process regression-accelerated QM/MM free energy simulations using atomic environment descriptors

ChemRxiv(2025)10.26434/chemrxiv-2025-hg8n7-v2

N/A

0DataRank · unranked

0 citations

Dongru Li, T.‐L. HO, Bryant Kim, Hysum Qazi, Xiaoliang Pan +3 more

Turn-on chemiluminescence probes and dual-amplification of signal for detection of amyloid beta species in vivo

Nature Communications(2020)10.1038/s41467-020-17783-4

N/A

0DataRank · unranked

121 citations

Wei Yin, Richard Van, Keyi Yin, Peng Wang, Chao Zheng +7 more

A Computational Modeling of ADLumin Chemiluminescence: Oxygenation and Dioxetanone Formation

ChemRxiv(2025)10.26434/chemrxiv-2025-ww011

N/A

0DataRank · unranked

0 citations

Chance Lander, Zheng Pei, Wai Tak Yip, Chongzhao Ran, Yihan Shao +1 more

Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations

Physical Chemistry Chemical Physics(2020)10.1039/d0cp04206d

N/A

0DataRank · unranked

21 citations

Zheng Pei, Jingheng Deng, Yuezhi Mao, Qin Wu, Zhibo Yang +5 more

Analysis and visualization of energy densities. II. Insights from linear-response time-dependent density functional theory calculations

Physical Chemistry Chemical Physics(2020)10.1039/d0cp04207b

N/A

0DataRank · unranked

16 citations

Junjie Yang, Jingheng Deng, Yuezhi Mao, Qin Wu, Zhibo Yang +5 more

Synthesis and pharmacokinetic study of a 11C-labeled cholesterol 24-hydroxylase inhibitor using ‘in-loop’ [11C]CO2 fixation method

Bioorganic & Medicinal Chemistry Letters(2020)10.1016/j.bmcl.2020.127068

N/A

0DataRank · unranked

11 citations

Jiahui Chen, Natalia Mast, Jian Rong, Xiaoyun Deng, Tuo Shao +9 more

Synthesis and preliminary evaluation of novel 11C-labeled GluN2B-selective NMDA receptor negative allosteric modulators

Acta Pharmacologica Sinica(2020)10.1038/s41401-020-0456-9

N/A

0DataRank · unranked

11 citations

Katsushi Kumata, Zhen Chen, Yiding Zhang, Jiahui Chen, Akiko Hatori +18 more

TD-DFT spin-adiabats with analytic nonadiabatic derivative couplings

The Journal of Chemical Physics(2020)10.1063/1.5126440

N/A

0DataRank · unranked

15 citations

Ethan Alguire, Shervin Fatehi, Yihan Shao, Joseph E. Subotnik, Nicole Bellonzi

How accurate are approximate quantum chemical methods at modelling solute–solvent interactions in solvated clusters?

Physical Chemistry Chemical Physics(2020)10.1039/c9cp06792b

N/A

0DataRank · unranked

38 citations

Bun Chan, Yihan Shao, Junming Ho, Junbo Chen

Synthesis and preliminary evaluation of 18F-labeled 1-(6,7-dimethyl-4-(methylamino)-1,3-dihydro-2H-pyrrolo[3,4-c]pyridin-2-yl)-2-(trans-2-(6-fluoropyridin-3-yl)cyclopropyl)ethan-1-one for imaging muscarinic acetylcholine receptor subtype 4

Tetrahedron Letters(2020)10.1016/j.tetlet.2020.152060

N/A

0DataRank · unranked

1 citations

Yiding Zhang, Jian Rong, Katsushi Kumata, Tuo Shao, Gangqiang Wang +11 more

Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference-Potential. 4. Adaptive QM/MM

ChemRxiv(2020)10.26434/chemrxiv.12764726.v2

N/A

0DataRank · unranked

2 citations

Wei Liu, Pengfei Li, Yan Mo, Wenxin Hu, Jun Zheng +4 more