Postdoctoral Researcher in Computational Pathology · Humanitas Research Hospital (IRCCS), Milan, Italy
Computational chemist and bioinformatician working at the interface of molecular modelling, spatial omics, and machine learning. My research focuses on developing reproducible computational frameworks for integrating multi-omics and bioimage data to understand tumour microenvironment dynamics and therapeutic response. I develop open-source software tools for virtual screening, molecular dynamics, and bioactivity prediction, with published applications in drug discovery and structural bioinformatics.
- Spatial omics, Imaging Mass Cytometry (IMC), and tumour microenvironment modelling
- Structure-based virtual screening and computational drug discovery
- Molecular dynamics simulations and free-energy profiling
- QSAR and machine learning for bioactivity and ADMET prediction
- Multi-omics data integration (RNA-seq, ATAC-seq, scRNA-seq)
- Reproducible and scalable computational pipelines
| Project | Description | Language | Publication |
|---|---|---|---|
| VSpipe-GUI | Interactive GUI for virtual screening and hit selection; integrates AutoDock Vina and AutoDock 4 with spatial filtering | |
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| BIOPREDICT | End-to-end QSAR framework for bioactivity (pIC50) prediction using Random Forest and PubChem fingerprints | |
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| COVID-19 Bioactivity Predictor | QSAR model + Streamlit app for predicting inhibitor potency against SARS-CoV-2 Replicase Polyprotein | |
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| MDSimulator | Python-tkinter GUI for setting up and running GROMACS molecular dynamics simulations | |
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| PyMOL Script Repository | Collection of PyMOL scripts for structural analysis, visualisation, and automation | |
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Hussain R., Hackett A.S., Álvarez-Carretero S., Tabernero L. (2024). VSpipe-GUI, An Interactive Graphical User Interface for Virtual Screening and Hit Selection. International Journal of Molecular Sciences, 25(4), 2002. DOI: 10.3390/ijms25042002
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Hussain R., Haider Z., Khalid H., Fatmi M.Q., Carradori S., Cataldi A., Zara S. (2023). Computational medicinal chemistry applications to target Asian-prevalent strain of hepatitis C virus. RSC Advances, 13(43), 30052–30070. DOI: 10.1039/D3RA04622B
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Hussain R., Khalid H., Fatmi M.Q. (2022). HCV genotype-specific drug discovery through structure-based virtual screening. Pure and Applied Chemistry. DOI: 10.1515/pac-2021-1104
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Hussain R., Khalid H., Fatmi M.Q. (2021). Molecular modelling approach of Serine Protease NS3-4A genotype 3a as a potential drug target of Hepatitis C Virus. Journal of Computational Biophysics and Chemistry, 20(6), 631–639.
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Basharat A.R., Iman K., Bibi Z., Hussain R., et al. (2019). SPECTRUM – A MATLAB toolbox for proteoform identification from top-down proteomics data. Scientific Reports – Nature, 9(1), 1–14. DOI: 10.1038/s41598-019-47724-1
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Ashraf M.U., Iman K., ..., Hussain R., et al. (2019). Evolution of efficacious pangenotypic Hepatitis C Virus therapies. Medicinal Research Reviews, 39(3), 1091–1136. DOI: 10.1002/med.21554
Show more publications (6)
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Khalid H., Hussain R., & Hafeez A. (2020). Virtual screening of piperidine-based small molecules against COVID-19. Lab-in-Silico, 1(2), 50–55.
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Arfan M., Siddiqui S.Z., ..., Hussain R., et al. (2018). Synthesis, in vitro and silico studies of S-alkylated triazole-3-thiols as cholinesterase inhibitors. Pakistan Journal of Pharmaceutical Sciences, 31(6), 2697–2708.
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Khalid H., Abbasi M.A., Hussain R., et al. (2017). Synthesis, spectral analysis and biological evaluation of 5-Substituted 1,3,4-oxadiazole-2-yl benzyl sulfide. Springer Books, Chapter 14, 221–238.
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Abubakar M., Bibi A., Hussain R., et al. (2016). Towards Providing Full Spectrum Antenatal Health Care in Low and Middle Income Countries. BIOSTEC 2016, Rome, Italy, 478–483.
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Mumtaz S., Hussain R., Rauf A., et al. (2014). Synthesis, molecular docking studies, and in vitro screening of barbiturates as antibacterial and cholinesterase inhibitors. Medicinal Chemistry Research, 23(6), 2715–2726.
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Khalid H., ..., Hussain R., et al. (2014). Synthesis, biological evaluation, and molecular docking of piperidine-4-carbohydrazide derivatives. Turkish Journal of Chemistry, 38(2), 189–201.
| Position | Institution | Period |
|---|---|---|
| Postdoctoral Researcher – Computational Pathology | Humanitas Research Hospital (IRCCS), Milan, Italy | 2026 – Present |
| Bioinformatician | Ayass BioScience LLC, TX, USA (Remote) | 2023 – 2025 |
| Software Developer (Contractor) – Computational Chemistry | Deep Waters LLC, NY, USA (Remote) | 2022 – 2023 |
| Visiting Postgraduate Researcher (IRSIP Fellow) | University of Manchester, UK | 2022 |
| Research Assistant – Drug Discovery | A.Z. Pharmaceuticals, Pakistan | 2016 – 2019 |
| Research Associate – Proteomics & Bioinformatics | Lahore University of Management Sciences, Pakistan | 2015 – 2016 |
| Award / Membership | Organisation | Year |
|---|---|---|
| Global Talent Endorsement | Royal Society, UK | 2025 |
| Registered Scientist (RSci) | Science Council, UK | 2025 |
| Magna Cum Laude | Forman Christian College (Chartered University) | 2023 |
| Intellectual Property – BIOPREDICT | Intellectual Property Organisation of Pakistan | 2023 |
| Intellectual Property – MDSimulator | Intellectual Property Organisation of Pakistan | 2023 |
| Member (MRSC) | Royal Society of Chemistry | 2023 – Present |
| Member | American Chemical Society | 2022 – Present |
| Certified Carpentries Instructor | The Carpentries, USA | 2022 – Present |
| International Research Support Initiative (IRSIP) | Higher Education Commission, Pakistan | 2022 |
| Journal | Publisher | Since |
|---|---|---|
| Molecular Diversity | Springer Nature | 2022 |
| International Journal of Biological Macromolecules | Elsevier | 2023 |
| RSC Advances | Royal Society of Chemistry | 2023 |
| Scientific Reports | Springer Nature | 2023 |
| BMC Chemistry | Springer Nature (BMC) | 2023 |
| In Silico Pharmacology | Springer Nature | 2023 |
| Discover Chemistry | Springer Nature | 2024 |
| BMC Immunology | Springer Nature (BMC) | 2026 |
