Contact

Open-source contributions

practical_cheminformatics_tutorials chembl_downloader

Research skills

• Molecular modeling
• Structured-based drug design
• Homology model building
• Homology model validation
• High throughput virtual screening
• Schrödinger (Maestro, Glide)
• Protein-ligand docking analysis
• Ligand-based drug design
• Pharmacophore screening
• Organic chemical synthesis
• Compound characterisations

Programming skills

Python
Polars
Pandas
NumPy
scikit-learn
Plotly
Matplotlib
R
tidyverse
RMarkdown / Quarto
Git
GitHub

Certification

• Data Science Professional Certificate (in Python) - authorised by IBM and verified by Coursera (from 9-11-2021 to 1-28-2022)

Volunteering work

• Rotating curator for @RLadiesGlobal community - @WeAreRLadies on Twitter from 10-24-2022 to 10-29-2022 via invitation by rotating curator team

Jennifer HY Lin

Cheminformatics projects

2024	Boosted trees - machine learning in drug discovery series 2.3.1 Using AdaBoost, XGBoost and Scikit-mol on ChEMBL data VS Code
2024	Random forest classifier - machine learning in drug discovery series 2.2.1 A random forest classifier model that used a different approach for imbalanced drug discovery data. First contribution to an open-source library, chembl_downloader, also occurred while working on this work. VS Code
2023	Random forest - machine learning in drug discovery series 2.2 A follow-up project on decision tree series using ChEMBL data - model building using scikit-learn with feature sections on imbalanced data, feature importances and hyperparameter tuning. VS Code
2023	Decision tree - machine learning in drug discovery series 2.1.1, series 2.1.2 & series 2.1.3 Application of decision tree on small molecule drug discovery data from ChEMBL database targeting acetylcholinesterase. VS Code
2023	Molecular visualisation (Molviz) web application - Shiny for Python web application framework , interactive data table Using Shiny for Python web application framework with interactive data table. VS Code
2023	Working with scaffolds in small molecules Manipulating SMILES strings using RDKit and Datamol. VS Code & RStudio IDE
2023	Shinylive app in Python - data preparation using Polars dataframe library, embedding app in Quarto document, using pyodide.http to import csv files Embedding app in Quarto document (web page) for compounds in COVID-19 clinical trials. RStudio IDE
2023	Shiny app in R A Shiny app was built based on data from ChEMBL database showing differences in physicochemical properties for small molecules in different max phases. RStudio IDE
2023	Pills dataset - part 1, part 2 & part 3 Polars & Pandas dataframe libraries, web scraping, text cleaning via Polars, with Rust used for visualization via Plotly in Jupyter-Evcxr on pills dataset from US National Library of Medicine (Python & Rust). Jupyter Lab & RStudio IDE
2022	Small molecules in ChEMBL database 1 - Parquet file in Polars dataframe library, 2 - Preprocessing data in Polars dataframe library, 3 - Building logistic regression model using scikit-learn & 4 - Evaluating logistic regression model in scikit-learn Polars dataframe library (with Python binding), scikit-learn & logistic regression used for ChEMBL database to predict max phases of small molecules. Jupyter Lab, RStudio IDE or VS Code
2022	Molecular similarities in selected COVID-19 antivirals Cheminformatics project on molecular similarities between selected COVID-19 antivirals by using RDKit. Jupyter notebook in Anaconda & RStudio IDE

Work experience

2022 \| 2007	Registered pharmacist Christchurch hospital pharmacy from 2019 to 2020 and community pharmacy from 2021 to 2022 (Canterbury, New Zealand), hospital pharmacy from 2012 to 2019 (NSW, Australia), hospital and community pharmacies from 2007 to 2012 (Canterbury, New Zealand)

Education

2019 \| 2015	Doctor of Philosophy University of Sydney - thesis title: The use of computer-aided drug design in small molecule drug discovery New South Wales, Australia
2014 \| 2012	Master of Philosophy University of Sydney - thesis title: Design, synthesis and testing of novel anti-cancer agents targeting secretary pathway calcium ATPase New South Wales, Australia
2006 \| 2003	Bachelor of Pharmacy University of Otago Otago, New Zealand

Publications

2022	Discovery of 2',6-Bis(4-hydroxybenzyl)-2-acetylcyclohexanone, a Novel FtsZ Inhibitor By Lin H-Y J, Battaje RR, Tan J, Doddareddy M, Dhaked HPS, Srivastava S, Hawkins BA, Al-Shdifat LMH, Hibbs DE, Panda D, Groundwater PW. Molecules. 2022; 27(20), 6993.
2017	A novel class of thiosemicarbazones show multi-functional activity for the treatment of Alzheimer's disease By Palanimuthu D, Poon R, Sahni S, Anjum R, Hibbs D, Lin J H-Y, Bernhardt PV, Kalinowski DS, Richardson DR. Eur J Med Chem. 2017; 139: 612-632.
2016	Identification of agents targeting FtsZ assembly By Panda D, Bhattacharya D, Gao QH, Oza PM, Lin J H-Y, Hawkins B, Hibbs DE, Groundwater PW Future Med Chem. 2016; 8(10):1111-32.
2015	Identification of dual PPARα/γ agonists and their effects on lipid metabolism By Gao Q, Hanh J, Váradi L, Cairns R, Sjöström H, Liao VW, Wood P, Balaban S, Ong JA, Lin J H-Y, Lai F, Hoy AJ, Grewal T, Groundwater PW, Hibbs DE Bioorg Med Chem. 2015; 23(24):7676-84.