Available for research collaborations

Hi, I'm Kashif Saleem

I decode complex biological systems through transcriptomics, multi-omics integration, and machine learning — building reproducible pipelines for biomedical discovery.

// transcriptomics // scRNA-seq // AMR
KS
Kashif Saleem
Computational Biologist
Sector H13, Islamabad, Pakistan
SCROLL
01
01 — About

Where biology meets computation

I'm a Computational Biologist & Bioinformatics Researcher with focused training in transcriptomics, multi-omics integration, and data-driven modeling of complex biological systems.

I design reproducible analysis pipelines and apply machine-learning methods to large-scale sequencing data — bulk and single-cell RNA-seq, metagenomics, and integrative systems biology. My research spans immune-mediated diseases, antimicrobial resistance, and infectious disease genomics.

I'm driven by hypothesis-led computational biology, methodological rigor, and the development of scalable, open, and interpretable analytical frameworks for biomedical research.

8+
Publications & Preprints
5+
Years of Research
2
Open-Source Tools
4
Research Roles
02
02 — Research Interests

What I work on

Hypothesis-driven, statistically rigorous, and biologically interpretable computational research at the intersection of omics and disease.

Transcriptomic & Single-Cell Analysis

Immune-mediated and infectious diseases, with emphasis on gene-regulatory mechanisms underlying disease heterogeneity and progression.

Multi-Omics Integration

Systems-level integration of bulk RNA-seq, single-cell transcriptomics, metagenomics, and metadata to infer biologically meaningful pathways and networks.

AMR & Host–Pathogen Modeling

Computational modeling of antimicrobial resistance, including population-level genomic surveillance, transmission patterns, and evolutionary analysis.

Reproducible Methods Development

Open, scalable, and interpretable computational methods for high-throughput biology — prioritizing statistical rigor and biological insight.

03
03 — Experience

Research trajectory

Research Scientist
National Institutes of Health (NIH), Islamabad — Public Health Laboratories
Jan 2025 — Present
  • Conduct genomic and transcriptomic analyses for infectious disease surveillance across hundreds of clinical and environmental samples.
  • Design reproducible NGS workflows (QC, alignment, variant calling, statistical analysis) using Linux pipelines and workflow managers.
  • Apply comparative genomics and metadata analysis to investigate transmission patterns and resistance trends.
  • Translate sequencing results into actionable public-health insights with wet-lab and epidemiology teams.
Research Assistant (Remote)
Green Biotec GmbH, Bremen, Germany
Jan 2025 — Dec 2025
  • Single-cell RNA-seq projects: preprocessing, QC, clustering, cell-type annotation, and differential expression.
  • Refined high-dimensional analysis workflows with emphasis on biological interpretation and reproducibility.
  • Contributed to training materials and hands-on workshops in single-cell genomics.
Technical Analyst — Bioinformatics (Remote)
Biocomputomics, Karachi, Pakistan
Mar 2024 — Jul 2025
  • Integrative bioinformatics across transcriptomics, genomics, and molecular modeling — supporting hypothesis generation.
  • Applied ML methods for feature selection and biological pattern discovery, prioritizing model interpretability.
  • Contributed computational analyses to peer-reviewed manuscripts in systems biology and drug discovery.
Bioinformatics Scientist
MERtech Company, Islamabad, Pakistan
2021 — 2024
  • Built and maintained pipelines for RNA-seq, metagenomics, and comparative genomics — emphasizing reproducibility and scalability.
  • Conducted statistical and systems-level analyses of high-throughput sequencing data.
  • Mentored undergraduate and graduate trainees in R, Python, and applied bioinformatics.
Co-Founder & Scientific Lead
Bioinfocamp
2024
  • Co-founded a training and research initiative focused on applied computational biology and reproducible data analysis.
  • Designed curricula on real biological datasets, statistical rigor, and open-science practices.
  • Supervised early-career researchers on academic-grade bioinformatics projects.
04
04 — Publications

Peer-reviewed work

Selected publications and preprints — including first-author contributions in transcriptomics, AMR, and computational drug discovery.

01
Decoding Systemic Lupus Erythematosus Pathogenesis: A Transcriptomics Approach to Identifying Key Molecular Mechanisms
Kashif Saleem, R. Z. Paracha, L. Khalid, A. Manzoor, D. Murad, M. Nisar, Nazar MD · Journal of Computer-Aided Molecular Design
Accepted
02
Designing of Sorafenib Analogues to Target c-RAF for the Management of Hepatocellular Carcinoma; Molecular Dynamics, mmPBSA Analysis and Integration of Machine Learning
S. Ijaz, R. Z. Paracha, M. Nisar, Kashif Saleem · Archives of Pharmacal Research
Published
03
Investigating the Evolution and Predicting the Resistance Trends Against Acinetobacter baumannii: An 18-Year Analysis Using Vivli AMR Surveillance Data
L. Khalid, Kashif Saleem, Z. Hussain, R. Z. Paracha, A. Hussain, I. Sajid · Computers in Biology and Medicine
Published
04
Towards Safer Antimicrobial Peptide Therapeutics: A Predictive–Generative Framework Targeting ESKAPE Pathogens
Z. Rashid, H. Ahmed, Kashif Saleem, M. R. U. Siddiqui · Springer Nature — Probiotics and Antimicrobial Proteins
Published
05
Feature Extraction from Genome Sequence Using Machine Learning
D. Murad, R. Z. Paracha, Kashif Saleem, B. Ishtiaq · Springer Nature — Book Chapter
Accepted
06
Computational Target Identification for Dengue Infection: Integrating Microarray, High-Throughput Sequencing, and Systems Biology Approaches
E. Fatima, R. Z. Paracha, Kashif Saleem, A. Manzoor, Nazar MD · Journal of Computer-Aided Molecular Design
Under Review
07
Integrative Analysis of Gut Microbiota and Host Phenotypic Traits in Broilers Fed Phytogenic and Organic Acid Formulations
Z. Rashid, H. Ahmed, Kashif Saleem · Annals of Microbiology
Under Review
08
Investigating the Anti-HSV-2 Potential of Phytochemicals from Polygonum aviculare using In-Silico Techniques
R. S. Butt, R. Z. Paracha, Kashif Saleem · PLOS One
Under Review
05
05 — Methods & Stack

Tools of the trade

High-Throughput Sequencing

Bulk RNA-seq scRNA-seq Metagenomics Variant Calling Gene-Set Enrichment Cell-Type Annotation Differential Expression

Statistical & ML Modeling

Hypothesis Testing Supervised ML Unsupervised ML Feature Selection Network Biology Multi-Omics Integration

Reproducible Computing

Nextflow Snakemake Docker Singularity Linux / HPC Cloud Pipelines

Programming

R Python Shell / Bash Git Markdown

Molecular Modeling

Protein–Ligand Docking Molecular Dynamics MM/PBSA Binding Free-Energy Sequence Features

Biological Interpretation

Pathway Analysis Functional Annotation Systems Biology Phenotype Integration Open Science
06
06 — Tools, Education & Credentials

Built, learned, earned

Software & Tools

PHEGEN
Gene prediction tool for antimicrobial resistance — exploratory analysis of metagenomic datasets.
Launch ↗
Wastewater-16S-rRNA-Amplicon-Surveillance-Pipeline
A complete, production-ready 16S rRNA amplicon sequencing pipeline designed for wastewater microbial surveillance.
In Progress

Education

M.S. in Bioinformatics — First Class Honors · CGPA 3.35/4.0
National University of Science and Technology (NUST), Islamabad
2023
Thesis: Computational Analysis of Systemic Lupus Erythematosus (SLE) using Sequencing, Systems Biology and Machine Learning approaches.
B.S. (Hons) in Bioinformatics — First Class Honors · CGPA 3.19/4.0
Government College University Faisalabad (GCUF)
2021
Thesis: In-Silico Mutational Analysis of BHLHA9 gene causing Complex Camptodactyly and Mesoaxial Synostotic Syndactyly.

Selected Certificates

IELTS Academic — Overall Band 6.5
Data Analysis with R — Google (2024)
Big Data, AI & Ethics — UC Davis (2024)
Generative AI with Large Language Models — DeepLearning.AI (2024)

Teaching & Mentorship

Instructor — R Programming for Bioinformatics, MERtech (2024)
Instructor — Python for Bioinformatics, MERtech (2024)
Trainer — Single-Cell RNA-seq Workshop, MERtech (2024)
Trainer — Scripting (Python & R), International Trainees (Qatar, Turkey, China, Pakistan; 2024)
07 — Contact

Let's build something scientific

Open to research collaborations, PhD opportunities, and interesting computational biology problems. The fastest way to reach me is by email.