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Hi, I am Rashid

Rashid Hussain, Ph.D., RSci, MRSC

Postdoctoral Research Associate
Humanitas Research Hospital.

I am a Postdoctoral Research Associate at Humanitas Research Hospital, Italy, working at the interface of bioinformatics, computational biology, and computational chemistry. My work involves developing computational tools and workflows to support development of the Sarcoma Microenvironment Score (SMS), an AI-based predictive and prognostic tool, build and maintain computational pipelines for microenvironment feature extraction and data integration, and perform statistical and machine learning analyses for model evaluation and reporting.

Leadership
Team Work
Hard Working
Fast Learner

Skills

Python
Python

I recently developed an open-source Python-based virtual screening toolkit with a cross-platform user-interactive GUI interface at The University of Manchester.
Linux
Linux

Using as the main operating system. Capable of writing bash/shell scripts.
R
R

Know basic R programming. Use to write small codes for accomplishing basic tasks.
Git
Git

Mostly, use Github for version control of the software program.
Cloud Computing
Cloud Computing

During my doctoral project, I ran virtual screening and molecular dynamics jobs using cloud computing.
MATLAB
MATLAB

I was part of the developement team of the project ‘SPECTRUM: A MATLAB Toolbox for Identifying Proteins from Top-down Proteomics Data’.
C++
C++

Know basic C/C++ programming. Used for contest programming and problem solving.
GROMACS
GROMACS

I have run MD Simulations of Holo-enzyme and Protein-Ligand complex at 50ns and 100ns during my doctoral studies.
PyMOL
PyMOL

Used PyMOL for visualizing macromolecules and studying protein-ligand interactions. Also used its plugin autodock.py for virtual screening.
RDKit
RDKit

Used RDKit for calculating physicochemical descriptors of compounds retreived from PubChem.
SQL
SQL

Know basics of storing, retreiving, and updating of the data from the databases.
Pandas
Pandas

I have used pandas for reading and writing data into the csv files fetched from PubChem.
Scikit-learn
Scikit-learn

I have used sklearn’s model selection module for splitting train-test data and applying RandomForest Regression. It was used in my project for building COVID QSAR model using machine learning.

Experience

1
Postdoctoral Researcher
Humanitas Research Hospital

Jan 2026 - Present, Italy

Computational pathology, bioinformatics, and AI-driven research

Responsibilities:
  • Support development of the Sarcoma Microenvironment Score (SMS), an AI-based predictive and prognostic tool
  • Build and maintain computational pipelines for microenvironment feature extraction and data integration
  • Perform statistical and machine learning analyses for model evaluation and reporting
University of Manchester (UoM)

Jan 2022 - Present, UK

Computational chemistry and bioinformatics research

Visiting Academic

Jul 2025 - Present

  • Develop and extend a Python-based virtual screening GUI (VSpipe) for molecular docking
  • Perform structure-based analyses, including molecular docking and protein modelling, to characterise drug–target interactions and resistance-associated variations
Visiting Postgraduate Researcher

Jan 2022 - Jun 2022

  • Developed VSpipe, a cross-platform Python application for virtual screening and hit selection
  • Deployed tool across Mac, Linux, and Windows environments
  • Contributed to publication in International Journal of Molecular Sciences
2
3
Bioinformatician
Ayass BioScience LLC

Jul 2023 - May 2025, USA (Remote)

Bioinformatics and AI-driven drug data workflows

Responsibilities:
  • Developed pipelines to fetch drug data from public databases via APIs
  • Integrated agentic AI to automate workflows and reduce manual intervention
  • Applied bioinformatics and machine learning techniques for transcriptome analysis
Software Developer (Contractor)
Deep Waters LLC

Nov 2022 - May 2023, USA (Remote)

Computational chemistry and software development

Responsibilities:
  • Developed a PyMOL plugin for water thermodynamics analysis using GIST and AMBER
  • Built and deployed a QSAR model for predicting bioactivity against receptor tyrosine kinases
4
5
Research Assistant
A.Z. Pharmaceuticals Company Limited

Feb 2016 - Dec 2019, Pakistan

Drug discovery and industrial research

Responsibilities:
  • Developed structure-based drug design pipelines and ligand-based pharmacophore models
  • Secured cGMP certification through regulatory compliance work
  • Collaborated with universities to support joint research initiatives
Research Associate
Lahore University of Management Sciences (LUMS)

Feb 2015 - Jan 2016, Pakistan

Bioinformatics and computational biology research

Responsibilities:
  • Designed GUI for MATLAB-based SPECTRUM toolbox and contributed to protein identification algorithms
  • Developed ligand-based pharmacophore models for HCV drug discovery
  • Managed lab operations and contributed to manuscript preparation and publication
6
7
Research Intern
National Center of Bioinformatics, Quaid-e-Azam University

Jun 2014 - Jan 2015, Pakistan

Bioinformatics and experimental research

Responsibilities:
  • Gained hands-on experience in experimental techniques including zebrafish models
  • Applied bioinformatics tools to identify conserved genomic regions

Publications

1
VSpipe-GUI, An Interactive Graphical User Interface for Virtual Screening and Hit Selection
International Journal of Molecular Sciences (2024)

2024 - DOI: 10.3390/ijms25042002, | Research Paper

Hussain, R., Hackett, A.S., Álvarez-Carretero, S., Tabernero, L.

Computational medicinal chemistry applications to target Asian-prevalent strain of hepatitis C virus
RSC Advances (2023)

2023 - DOI: 10.1039/D3RA04622B, | Research Paper

Hussain, R., Haider, Z., Khalid, H., Fatmi, M. Q., Carradori, S., Cataldi, A., Zara, S.

2
3
HCV genotype-specific drug discovery through structure-based virtual screening
Pure and Applied Chemistry (2022)

2022 - DOI: 10.1515/pac-2021-1104, | Research Paper

Hussain, R., Khalid, H., Fatmi, M. Q.

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 (2021)

2021 - Vol. 20, No. 06, pp. 631-639, | Research Paper

Hussain, R., Khalid, H., Fatmi, M. Q.

4
5
Virtual screening of piperidine-based small molecules against COVID-19
Lab-in-Silico (2020)

2020 - DOI: 10.22034/lins20012050, | Research Paper

Khalid, H., Hussain, R., Hafeez, A.

SPECTRUM - A MATLAB toolbox for proteoform identification from top-down proteomics data
Scientific Reports - Nature (2019)

2019 - DOI: 10.1038/s41598-019-47724-1, | Research Paper

Basharat, A. R., Iman, K., Bibi, Z., Hussain, R., Kabir, H. G., Shahid, A., Humayun, M., Hayat, H. A., Mustafa, M., Shoaib, M. A., Ullah, Z., Zarina, S., Ahmed, S., Uddin, E., Hamera, S., Ahmad, F., & Chaudhary, S. U.

6
7
Evolution of efficacious pangenotypic Hepatitis C Virus therapies
Medicinal Research Reviews (2019)

2019 - DOI: 10.1002/med.21554, | Review Paper

Ashraf, M. U., Iman, K., Khalid, M. F., Shafi, T., Salman, H. M., Rafi, M., Javaid, N., Hussain, R., Ahmad, F., Shahzad-ul-Hussan, S., Mirza, S., Shafiq, M., Afzal, S., Idrees, M., Hamera, S., Anwar, S., Qazi, R. Qureshi, S. A., Chaudhary, S. U.

Synthesis, in vitro and silico studies of S-alkylated 5-(4-methoxyphenyl)-4-phenyl-4H-1, 2, 4-triazole-3-thiols as cholinesterase inhibitors
Pakistan Journal of Pharmaceutical Sciences (2018)

2018 - Vol. 31, No. 06, pp. 2697-2708, | Research Paper

Arfan, M., Siddiqui, S.Z., Abbasi, M.A., ur Rehman, A., Shah, S.A.A., Ashraf, M., Rehman, J., Saleem, R. S. Z., Khalid, H., Hussain, R., Khan, U.

8
9
Synthesis, spectral analysis and biological evaluation of 5-Substituted 1,3,4-oxadiazole-2-yl-4-(piperidin-1-ylsulfonyl)benzyl sulfide
Emerging Trends in Chemical Sciences (2017)

2017 - DOI: 10.1007/978-3-319-60408-4_14, | Book Chapter

Khalid, H., Abbasi, M. A., Hussain, R., Malik, A., Ashraf, M., & Fatmi, M. Q.

Towards Providing Full Spectrum Antenatal Health Care in Low and Middle Income Countries
BIOSTEC 2016

2016 - HEALTHINF, pp. 478-483, | Conference Paper

Abubakar, M., Bibi, A., Hussain, R., Bibi, Z., Gul, A., Bashir, Z., Arshad, S.N., Uppal, S.U., Chaudhary, S. U.

10
11
Synthesis, molecular docking studies, and in vitro screening of barbiturates/thiobarbiturates as antibacterial and cholinesterase inhibitors
Medicinal Chemistry Research (2014)

2014 - DOI: 10.1007/s00044-013-0847-2, | Research Paper

Mumtaz, S., Hussain, R., Rauf, A., Fatmi, M. Q., Bokhari, H., Oelgemöller, M., & Qureshi, A. M.

Synthesis, biological evaluation, and molecular docking of N'-(Aryl/alkylsulfonyl)-1-(phenylsulfonyl) piperidine-4-carbohydrazide derivatives
Turkish Journal of Chemistry (2014)

2014 - DOI: 10.3906/kim-1303-89, | Research Paper

Khalid, H., Rehman, A. U., Abbasi, M. A., Hussain, R., Khan, K. M., Ashraf, M., Ejaz, S.A., & Fatmi, M. Q.

12

Education
Forman Christian College (A Chartered University)
2017 - 2023
Ph.D. in Chemistry
  • Areas - Computational Chemistry, Bioinformatics, Cheminformatics, Software Development
  • **Award: Magna Cum Laude (Higher Honors)**
  • Thesis - Computer-aided drug design and synthesis of HCV NS3 protease inhibitors
  • Supervisors - Dr. Hira Khalid, Prof. M. Qaiser Fatmi, Prof. Lydia Tabernero
COMSATS University Islamabad
2011 - 2013
M.S. in Bioinformatics
  • Areas - Bioinformatics, Bash Scripting, Cheminformatics
  • Thesis - Rationalizing ligand-protein interactions and identifying cholinesterase
  • Supervisor - Prof. M. Qaiser Fatmi
COMSATS University Islamabad
2006 - 2010
B.S. in Bioinformatics
  • Areas - Bioinformatics, Phylogenetic Data Analysis
  • Thesis - Phylogenetic analysis of major protein-coding genes of Geminiviridae, a single-stranded DNA virus family
  • Supervisor - Prof. Muhammad Zeeshan Hyder

Achievements

Best Poster Award

Marathon Race Winner

Secured Research Fellowship

Projects

SPECTRUM
SPECTRUM
Contributor

A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data.

professional MATLAB
Star
Bioactivity Predictor
Bioactivity Predictor
Developer

Machine Learning based QSAR model for COVID19 Replicase Polyprotein to predict pIC50 of a given compound.

professional machine-learning
Star
Personal Blog
Personal Blog
Developer

Portfolio and personal blog is created using hugo theme and deployed on GitHub.
https://rashid-bioinfo.github.io/

professional GitHub
Star
Notepad app
Notepad app
Developer

A notepad GUI app is developed in Python-Tkinter.

academic Python
Star

Accomplishments

Certificate - The Unix Workbench
Johns Hopkins University Jul 8, 2022

I really enjoyed this course. The course covers from very basic to advance topics in Unix. I have learnt regular expressions, bash scripting, GitHub, and Cloud Computing. I also made account on DigitalOcean and accessed the system remotely. Overall very good experience and I have learnt a lot in this course.

View Certificate
Certificate - What is Data Science?
IBM Jun 14, 2022

In this course I have got basic understanding of data science. I got the chance to know about big data, data mining, deep learning, regession etc. I also studied about Hadoop which is a framework for distributed processing of large data sets. I also got the chance to know about IBM cloud features, created IBM cloud account and explored Watson Studio Instance and Jupyter.

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Symposium - Introduction to Structure-Based Drug Design using MOE
Chemical Computing Group Jun 09, 2022

This was a three hours long online symposium with focus on using Molecular Operating Environment (MOE), a software for computer aided drug design. During the session, a case study for structure based drug design of an Epidermal Growth Factor (PDB ID: 1M17) was followed. The key concepts regarding protein-ligand representation, compound optimization, docking and analysing the docking results through scoring and generated fingerprints were discussed.

Virtual Drug Discovery Symposium 2021
LUMS Nov 01, 2021

This was a one day online symposium with a focus on virtual drug discovery. Many renowned scientists across the globe gave their talks. The core concepts discussed in the talks were about the current breakthrough in drug design and discovery and future challanges.

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Certificate - Introduction to Molecular Modeling in Drug Discovery
Schrodinger Dec 2020 - Jan 2021

In this course I have got experience of industry-leading computational molecular modeling tools used to aid in drug discovery and design. In average this course took 25 hours over a span of 5 weeks to complete. In addition to utilizing modern techniques such as active learning and multimodal teaching, I have also got chance to get hands-on with Schrödinger’s Maestro and LiveDesign.

View Certificate

Recent Posts

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Managing References & Bibliography

Online session for explaining thesis writing and hands on training on Mendeley, a software for managing references and bibliography.

This webinar is about managing references in your thesis or manuscript. Please watch the following videos, they will guide you right from installing mendeley software to inserting and managing references and bibliography in your documents.

October 6, 2020 Read
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Homology Modeling

Online tutorials for Homology Modeling using Modeller tool.

This tutorial series is about homology modeling using Modeller. Please watch the following videos, the videos are created to guide each step involved in homology modeling so that even naive user/viewer can also benefit from this effort.

June 15, 2020 Read
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DOCKING - Computer aided drug design

Online tutorials for performing docking against a protein in structure based drug design.

This tutorial series is about peforming docking using Autodock tools. Please watch the following videos, the videos are created to guide each step involved in docking so that naive user/viewer can also benefit from this effort.

June 6, 2020 Read