Rachel Liu

Tagline:Associate Professor @ RCEES | Ph.D. in Computational Drug Design

Santa Clara, CA, USA

About Me

I am an Associate Professor at RCEES with training in computational drug design, specializing in the application of machine learning and AI to problems in environmental chemistry and toxicology.

Education

Doctor of Philosophy (Ph.D.)
from: 2010, until: 2015
Field of study:Computational Drug DesignSchool:Shanghai Institute of Materia MedicaLocation:Shanghai

Publications

Machine learning for membrane bioreactor research: principles, methods, applications, and a tutorial
Journal ArticlePublisher:Frontiers of Environmental Science & EngineeringDate:2025
Authors:
Yizhe LaiKang XiaoYifan HeXian LiuJihua TanWenchao XueAiqian ZhangXia Huang
Nontarget Screening Analysis Combined with Computational Toxicology: A Promising Solution for Identification and Risk Assessment of Environmental Pollutants in the Big Data Era
Journal ArticlePublisher:Environmental Science & TechnologyDate:2025
Authors:
Pengyang LiBao ZhuJie FuXian LiuKai HuangWenxiao PanQiao XueHaiyan ZhangAiqian ZhangJianjie Fuothers
Development of an Interpretable Machine Learning Model for Neurotoxicity Prediction of Environmentally Related Compounds
Journal ArticlePublisher:Environmental Science & TechnologyDate:2025
Authors:
Yuxing HaoZhihui DuanLizheng LiuQiao XueWenxiao PanXian LiuAiqian ZhangJianjie Fu
Integrating Non-Targeted Mass Spectrometry and Machine Learning for the Classification of Organic and Conventionally Grown Agricultural Products: A Case Study on Tomatoes
Journal ArticlePublisher:Journal of Agricultural and Food ChemistryDate:2025
Authors:
Xiao YunXiaoxiao HanXin ZhangWenxiao PanQiao XueXian LiuJianjie FuRichard RöttgerAiqian Zhang
From Nuclear Receptors to GPCRs: a Deep Transfer Learning Approach for Enhanced Environmental Estrogen Recognition
Journal ArticlePublisher:Environmental Science & TechnologyDate:2025
Authors:
Tingji YaoJiaqi LuoXiaoxiao HanHang YiHuazhou ZhangWenxiao PanQiao XueXian LiuJianjie FuAiqian Zhang
From High Resolution Tandem Mass Spectrometry to Pollutant Toxicity AI-Based Prediction: A Case Study of 7 Endocrine Disruptors Endpoints
Journal ArticlePublisher:Environmental Science & TechnologyDate:2025
Authors:
Xin ZhangXiaoxiao HanTongtong XiangYanna LiuWenxiao PanQiao XueXian LiuJianjie FuAiqian ZhangGuangbo Quothers
Advancing toxicity AI-based prediction with multilevel systems biology: a case study on genotoxicity
Journal ArticlePublisher:Briefings in BioinformaticsDate:2025
Authors:
Xin ZhangHuazhou ZhangXiao YunWenxiao PanQiao XueXian LiuJianjie FuAiqian Zhang
Implications of VOC oxidation in atmospheric chemistry: development of a comprehensive AI model for predicting reaction rate constants
Journal ArticlePublisher:Atmospheric Chemistry and PhysicsDate:2025
Authors:
Xin ZhangJiaqi LuoWenxiao PanQiao XueXian LiuJianjie FuAiqian ZhangGuibin Jiang
First-principles study on the heterogeneous formation of environmentally persistent free radicals (EPFRs) over α-Fe2O3 (0001) surface: Effect of oxygen vacancy
Journal ArticlePublisher:Journal of Environmental SciencesDate:2024
Authors:
Wenxiao PanShuming HeQiao XueXian LiuJianjie FuKang XiaoAiqian Zhang
Multiscale computational simulation of pollutant behavior at water interfaces
Journal ArticlePublisher:Water ResearchDate:2024
Authors:
Qiao XueZhiyue JiaoWenxiao PanXian LiuJianjie FuAiqian Zhang
Deciphering exogenous chemical carcinogenicity through interpretable deep learning: A novel approach for evaluating atmospheric pollutant hazards
Journal ArticlePublisher:Journal of Hazardous MaterialsDate:2024
Authors:
Huazhou ZhangHang YiYuxing HaoLu ZhaoWenxiao PanQiao XueXian LiuJianjie FuAiqian Zhang
ChemNTP: Advanced Prediction of Neurotoxicity Targets for Environmental Chemicals Using a Siamese Neural Network
Journal ArticlePublisher:Environmental Science & TechnologyDate:2024
Authors:
Lingjing ZhangTingji YaoJiaqi LuoHang YiXiaoxiao HanWenxiao PanQiao XueXian LiuJianjie FuAiqian Zhang
Precisely identifying the sources of magnetic particles by hierarchical classification-aided isotopic fingerprinting
Journal ArticlePublisher:Environmental Science & TechnologyDate:2024
Authors:
Hang YangXuezhi YangQinghua ZhangDawei LuWeichao WangHuazhou ZhangYunbo YuXian LiuAiqian ZhangQian Liuothers
CatNet: Sequence-based deep learning with cross-attention mechanism for identifying endocrine-disrupting chemicals
Journal ArticlePublisher:Journal of Hazardous MaterialsDate:2024
Authors:
Lu ZhaoQiao XueHuazhou ZhangYuxing HaoHang YiXian LiuWenxiao PanJianjie FuAiqian Zhang
Theoretical Investigation of Cytochrome P450 Enzyme-Mediated Biotransformation Mechanism of BHPF: Unveiling the Metabolic Safety Aspects of an Alternative to BPA
Journal ArticlePublisher:Environment & HealthDate:2024
Authors:
Wenxiao PanShuming HeYinzheng YangYongdie YangQiao XueXian LiuJianjie FuAiqian Zhang
Unveiling key mechanisms: Transcriptomic meta-analysis of diverse nanomaterial applications addressing biotic and abiotic stresses in Arabidopsis thaliana
Journal ArticlePublisher:Science of The Total EnvironmentDate:2024
Authors:
Yining WuYvjie WangXian LiuChengdong Zhang
New mechanism for the apoptosis of human neuroblastoma cells by the interaction between fluorene-9-bisphenol and the G protein-coupled estrogen receptor 1
Journal ArticlePublisher:Environmental Science & TechnologyDate:2024
Authors:
Xiuchang LiuZhi ChengXueliang ShangHuazhou ZhangXian LiuWenxiao PanJianjie FuQiao XueAiqian Zhang
Exogenous chemicals impact virus receptor gene transcription: Insights from deep learning
Journal ArticlePublisher:Environmental Science & TechnologyDate:2023
Authors:
Xian LiuYunhe GuoWenxiao PanQiao XueJianjie FuGuangbo QuAiqian Zhang
Dynamic behavior and interaction mechanism of soil organic matter in water systems: a coarse-grained molecular dynamics study
Journal ArticlePublisher:Environmental Science & TechnologyDate:2023
Authors:
Qiao XueZhiyue JiaoXian LiuWenxiao PanJianjie FuAiqian Zhang
Machine learning strategy on activation energy of environmental heterogeneous reactions and its application to atmospheric formation of typical montmorillonite-bound phenoxy radicals
Journal ArticlePublisher:Science of The Total EnvironmentDate:2023
Authors:
Wenxiao PanJiamin ChangShuming HeXian LiuJianjie FuAiqian Zhang
Machine learning-aided metallomic profiling in serum and urine of thyroid cancer patients and its environmental implications
Journal ArticlePublisher:Science of the Total EnvironmentDate:2023
Authors:
Zigu ChenXian LiuWeichao WangLuyao ZhangWeibo LingChao WangJie JiangJiayi SongYuan LiuDawei Luothers
Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock
Journal ArticlePublisher:Ecotoxicology and environmental safetyDate:2022
Authors:
Qiao XueXian LiuPaul RussellJin LiWenxiao PanJianjie FuAiqian Zhang
Identification of two-dimensional copper signatures in human blood for bladder cancer with machine learning
Journal ArticlePublisher:Chemical scienceDate:2022
Authors:
Weichao WangXian LiuChangwen ZhangFei ShengShanjun SongPenghui LiShaoqing DaiBin WangDawei LuLuyao Zhangothers
Computational Insights into the Allosteric Effect and Dynamic Structural Features of the SARS-COV-2 Spike Protein
Journal ArticlePublisher:Chemistry–A European JournalDate:2022
Authors:
Qiao XueXian LiuWenxiao PanAiqian ZhangJianjie FuGuibin Jiang
Data-driven machine learning in environmental pollution: gains and problems
Journal ArticlePublisher:Environmental science & technologyDate:2022
Authors:
Xian LiuDawei LuAiqian ZhangQian LiuGuibin Jiang
Seppcnet: deeping learning on a 3d surface electrostatic potential point cloud for enhanced toxicity classification and its application to suspected environmental estrogens
Journal ArticlePublisher:Environmental Science & TechnologyDate:2021
Authors:
Liguo WangLu ZhaoXian LiuJianjie FuAiqian Zhang
In silico health effect prioritization of environmental chemicals through transcriptomics data exploration from a chemo-centric view
Journal ArticlePublisher:Science of the Total EnvironmentDate:2021
Authors:
Xian LiuHuazhou ZhangQiao XueWenxiao PanAiqian Zhang
Major influence of hydroxyl and nitrate radicals on air pollution by environmentally persistent free radicals
Journal ArticlePublisher:Environmental Chemistry LettersDate:2021
Authors:
Wenxiao PanJiamin ChangShuming HeQiao XueXian LiuJianjie FuAiqian Zhang
Estrogenic activity of benzotriazole UV stabilizers evaluated through in vitro assays and computational studies
Journal ArticlePublisher:Science of The Total EnvironmentDate:2020
Authors:
Hongru FengHuiming CaoJuan LiHaiyan ZhangQiao XueXian LiuAiqian ZhangJianjie Fu
The formation of PBDFs from the ortho-disubstituted phenol precursors: A comprehensive theoretical study on the PBDD/Fs formation from 2, 4, 6-tribromophenol
Journal ArticlePublisher:Science of The Total EnvironmentDate:2020
Authors:
Jiamin ChangWenxiao PanXian LiuQiao XueJianjie FuAiqian Zhang
A novel computational solution to the health risk assessment of air pollution via joint toxicity prediction: A case study on selected PAH binary mixtures in particulate matters
Journal ArticlePublisher:Ecotoxicology and Environmental SafetyDate:2019
Authors:
Xian LiuHuazhou ZhangWenxiao PanQiao XueJianjie FuGuorui LiuMinghui ZhengAiqian Zhang
Prenatal exposure to per-and polyfluoroalkyl substances (PFASs) and association between the placental transfer efficiencies and dissociation constant of serum proteins–PFAS complexes
Journal ArticlePublisher:Environmental science & technologyDate:2019
Authors:
Ke GaoTaifeng ZhuangXian LiuJianjie FuJingxing ZhangJie FuLiguo WangAiqian ZhangYong LiangMaoyong Songothers
Interfacial formation of environmentally persistent free radicals—A theoretical investigation on pentachlorophenol activation on montmorillonite in PM2. 5
Journal ArticlePublisher:Ecotoxicology and Environmental SafetyDate:2019
Authors:
Wenxiao PanJiamin ChangXian LiuQiao XueJianjie FuAiqian Zhang
The effect of structural diversity on ligand specificity and resulting signaling differences of estrogen receptor α
Journal ArticlePublisher:Chemical Research in ToxicologyDate:2019
Authors:
Qiao XueXian LiuXiu-Chang LiuWen-Xiao PanJian-Jie FuAi-Qian Zhang
Distinguishing the sources of silica nanoparticles by dual isotopic fingerprinting and machine learning
Journal ArticlePublisher:Nature CommunicationsDate:2019
Authors:
Xuezhi YangXian LiuAiqian ZhangDawei LuGang LiQinghua ZhangQian LiuGuibin Jiang
Length-specific occurrence and profile of perfluoroalkyl acids (PFAAs) in animal protein feeds
Journal ArticlePublisher:Journal of Hazardous MaterialsDate:2019
Authors:
Xiaomin LiKe GaoShujun DongXian LiuKehan FuPeilong WangAiqian ZhangXiaoou SuJianjie Fu
Inhibition of thrombin by functionalized C60 nanoparticles revealed via in vitro assays and in silico studies
Journal ArticlePublisher:Journal of Environmental SciencesDate:2018
Authors:
Yanyan LiuJianjie FuWenxiao PanQiao XueXian LiuAiqian Zhang
Theoretical study on the formation mechanism of polychlorinated dibenzothiophenes/thianthrenes from 2-chlorothiophenol molecules
Journal ArticlePublisher:Journal of Environmental SciencesDate:2018
Authors:
Xiaoqing YuJiamin ChangXian LiuWenxiao PanAiqian Zhang
In silico ADME/T modelling for rational drug design
Journal ArticlePublisher:Quarterly reviews of biophysicsDate:2015
Authors:
Yulan WangJing XingYuan XuNannan ZhouJianlong PengZhaoping XiongXian LiuXiaomin LuoCheng LuoKaixian Chenothers
Combinatorial pharmacophore modeling of multidrug and toxin extrusion transporter 1 inhibitors: a theoretical perspective for understanding multiple inhibitory mechanisms
Journal ArticlePublisher:Scientific ReportsDate:2015
Authors:
Yuan XuXian LiuYulan WangNannan ZhouJianlong PengLikun GongJing RenCheng LuoXiaomin LuoHualiang Jiangothers
TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds
Journal ArticlePublisher:BioinformaticsDate:2015
Authors:
Xian LiuYuan GaoJianlong PengYuan XuYulan WangNannan ZhouJing XingXiaomin LuoHualiang JiangMingyue Zheng
Combinatorial pharmacophore-based 3D-QSAR analysis and virtual screening of FGFR1 inhibitors
Journal ArticlePublisher:International Journal of Molecular SciencesDate:2015
Authors:
Nannan ZhouYuan XuXian LiuYulan WangJianlong PengXiaomin LuoMingyue ZhengKaixian ChenHualiang Jiang
In Silico target fishing: addressing a “Big Data” problem by ligand-based similarity rankings with data fusion
Journal ArticlePublisher:Journal of cheminformaticsDate:2014
Authors:
Xian LiuYuan XuShanshan LiYulan WangJianlong PengCheng LuoXiaomin LuoMingyue ZhengKaixian ChenHualiang Jiang
Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies
Journal ArticlePublisher:Acta Pharmacologica SinicaDate:2013
Authors:
Jing LiYun DuXian LiuQian-cheng ShenAi-long HuangMing-yue ZhengXiao-min LuoHua-liang Jiang
Identification of novel small molecules as inhibitors of hepatitis C virus by structure-based virtual screening
Journal ArticlePublisher:International Journal of Molecular SciencesDate:2013
Authors:
Jing LiXian LiuShanshan LiYulan WangNannan ZhouCheng LuoXiaomin LuoMingyue ZhengHualiang JiangKaixian Chen
Structure-based design and synthesis of C-1-and C-4-modified analogs of zanamivir as neuraminidase inhibitors
Journal ArticlePublisher:Journal of Medicinal ChemistryDate:2013
Authors:
Enguang FengWoo-Jin ShinXuelian ZhuJian LiDeju YeJiang WangMingyue ZhengJian-Ping ZuoKyoung Tai NoXian Liuothers
Computational methods for drug design and discovery: focus on China
Journal ArticlePublisher:Trends in pharmacological sciencesDate:2013
Authors:
Mingyue ZhengXian LiuYuan XuHonglin LiCheng LuoHualiang Jiang
In silico prediction of cytochrome P450-mediated site of metabolism (SOM)
Journal ArticlePublisher:Protein and Peptide LettersDate:2013
Authors:
Xian LiuQiancheng ShenJing LiShanshan LiCheng LuoWeiliang ZhuXiaomin LuoMingyue ZhengHualiang Jiang
Non-covalent interactions with aromatic rings: current understanding and implications for rational drug design
Journal ArticlePublisher:Current pharmaceutical designDate:2013
Authors:
Shanshan LiYuan XuQiancheng ShenXian LiuJing LuYadong ChenTao LuCheng LuoXiaomin LuoMingyue Zhengothers
Combinatorial pharmacophore modeling of organic cation transporter 2 (OCT2) inhibitors: insights into multiple inhibitory mechanisms
Journal ArticlePublisher:Molecular pharmaceuticsDate:2013
Authors:
Yuan XuXian LiuShanshan LiNannan ZhouLikun GongCheng LuoXiaomin LuoMingyue ZhengHualiang JiangKaixian Chen

Contact

GitHub

https://github.com/xliu-deep

https://www.linkedin.com/in/rachel-liu-ca/

Google Scholar

https://scholar.google.com/citations?user=5QE9LyIAAAAJ&hl=en

contents:

Rachel Liu

About Me

Education

Doctor of Philosophy (Ph.D.)

Publications

Machine learning for membrane bioreactor research: principles, methods, applications, and a tutorial

Nontarget Screening Analysis Combined with Computational Toxicology: A Promising Solution for Identification and Risk Assessment of Environmental Pollutants in the Big Data Era

Development of an Interpretable Machine Learning Model for Neurotoxicity Prediction of Environmentally Related Compounds

Integrating Non-Targeted Mass Spectrometry and Machine Learning for the Classification of Organic and Conventionally Grown Agricultural Products: A Case Study on Tomatoes

From Nuclear Receptors to GPCRs: a Deep Transfer Learning Approach for Enhanced Environmental Estrogen Recognition

From High Resolution Tandem Mass Spectrometry to Pollutant Toxicity AI-Based Prediction: A Case Study of 7 Endocrine Disruptors Endpoints

Advancing toxicity AI-based prediction with multilevel systems biology: a case study on genotoxicity

Implications of VOC oxidation in atmospheric chemistry: development of a comprehensive AI model for predicting reaction rate constants

First-principles study on the heterogeneous formation of environmentally persistent free radicals (EPFRs) over α-Fe2O3 (0001) surface: Effect of oxygen vacancy

Multiscale computational simulation of pollutant behavior at water interfaces

Deciphering exogenous chemical carcinogenicity through interpretable deep learning: A novel approach for evaluating atmospheric pollutant hazards

ChemNTP: Advanced Prediction of Neurotoxicity Targets for Environmental Chemicals Using a Siamese Neural Network

Precisely identifying the sources of magnetic particles by hierarchical classification-aided isotopic fingerprinting

CatNet: Sequence-based deep learning with cross-attention mechanism for identifying endocrine-disrupting chemicals

Theoretical Investigation of Cytochrome P450 Enzyme-Mediated Biotransformation Mechanism of BHPF: Unveiling the Metabolic Safety Aspects of an Alternative to BPA

Unveiling key mechanisms: Transcriptomic meta-analysis of diverse nanomaterial applications addressing biotic and abiotic stresses in Arabidopsis thaliana

New mechanism for the apoptosis of human neuroblastoma cells by the interaction between fluorene-9-bisphenol and the G protein-coupled estrogen receptor 1

Exogenous chemicals impact virus receptor gene transcription: Insights from deep learning

Dynamic behavior and interaction mechanism of soil organic matter in water systems: a coarse-grained molecular dynamics study

Machine learning strategy on activation energy of environmental heterogeneous reactions and its application to atmospheric formation of typical montmorillonite-bound phenoxy radicals

Machine learning-aided metallomic profiling in serum and urine of thyroid cancer patients and its environmental implications

Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock

Identification of two-dimensional copper signatures in human blood for bladder cancer with machine learning

Computational Insights into the Allosteric Effect and Dynamic Structural Features of the SARS-COV-2 Spike Protein

Data-driven machine learning in environmental pollution: gains and problems

Seppcnet: deeping learning on a 3d surface electrostatic potential point cloud for enhanced toxicity classification and its application to suspected environmental estrogens

In silico health effect prioritization of environmental chemicals through transcriptomics data exploration from a chemo-centric view

Major influence of hydroxyl and nitrate radicals on air pollution by environmentally persistent free radicals

Estrogenic activity of benzotriazole UV stabilizers evaluated through in vitro assays and computational studies

The formation of PBDFs from the ortho-disubstituted phenol precursors: A comprehensive theoretical study on the PBDD/Fs formation from 2, 4, 6-tribromophenol

A novel computational solution to the health risk assessment of air pollution via joint toxicity prediction: A case study on selected PAH binary mixtures in particulate matters

Prenatal exposure to per-and polyfluoroalkyl substances (PFASs) and association between the placental transfer efficiencies and dissociation constant of serum proteins–PFAS complexes

Interfacial formation of environmentally persistent free radicals—A theoretical investigation on pentachlorophenol activation on montmorillonite in PM2. 5

The effect of structural diversity on ligand specificity and resulting signaling differences of estrogen receptor α

Distinguishing the sources of silica nanoparticles by dual isotopic fingerprinting and machine learning

Length-specific occurrence and profile of perfluoroalkyl acids (PFAAs) in animal protein feeds

Inhibition of thrombin by functionalized C60 nanoparticles revealed via in vitro assays and in silico studies

Theoretical study on the formation mechanism of polychlorinated dibenzothiophenes/thianthrenes from 2-chlorothiophenol molecules

In silico ADME/T modelling for rational drug design

Combinatorial pharmacophore modeling of multidrug and toxin extrusion transporter 1 inhibitors: a theoretical perspective for understanding multiple inhibitory mechanisms

TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds

Combinatorial pharmacophore-based 3D-QSAR analysis and virtual screening of FGFR1 inhibitors

In Silico target fishing: addressing a “Big Data” problem by ligand-based similarity rankings with data fusion

Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies

Identification of novel small molecules as inhibitors of hepatitis C virus by structure-based virtual screening

Structure-based design and synthesis of C-1-and C-4-modified analogs of zanamivir as neuraminidase inhibitors

Computational methods for drug design and discovery: focus on China

In silico prediction of cytochrome P450-mediated site of metabolism (SOM)

Non-covalent interactions with aromatic rings: current understanding and implications for rational drug design

Combinatorial pharmacophore modeling of organic cation transporter 2 (OCT2) inhibitors: insights into multiple inhibitory mechanisms

Contact