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USD 80 /hr

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Hire Kashif S.

Pakistan

USD 80 /hr

Bioinformatics Consultant — Single-cell RNA-seq, Bulk Transcriptomics & Reproducible Pipelines | 9 Peer-Reviewed Publica

Profile Summary

Computational biologist with 5+ years of hands-on experience in transcriptomics, multi-omics integration, and reproducible bioinformatics pipelines. Currently a Research Scientist at the National Institutes of Health (Pakistan), with prior remote roles supporting biotech and research groups in Germany and Pakistan. Nine peer-reviewed publications, several as first author. I work end-to-end on single-cell RNA-seq, bulk RNA-seq, metagenomics, and antimicrobial resistance projects — from raw sequencing data through to publication-ready figures and methods. My deliverables are built to survive peer review: clean code, transparent QC, defensible statistical choices, and biological interpretation grounded in the literature. What I deliver: • Single-cell RNA-seq analysis (Seurat, Scanpy) — QC, integration, clustering, cell-type annotation, differential expression, trajectory inference • Bulk RNA-seq differential expression (DESeq2, edgeR, limma-voom) with GSEA / GO / KEGG pathway analysis • Reproducible Nextflow and Snakemake pipelines, containerized with Docker / Singularity • Metagenomic profiling and antimicrobial resistance gene detection • Manuscript methods writing, figure generation, and pre-submission analysis review Recent work includes transcriptomics analysis of Systemic Lupus Erythematosus (first-author, Journal of Computer-Aided Molecular Design), 18-year evolutionary analysis of Acinetobacter baumannii AMR (Computers in Biology and Medicine), and multi-omics chromatin regulation in thymic epithelial cells (PLOS One). I also developed PHEGEN, an open-source tool for AMR gene prediction from metagenomic data. I'm comfortable working independently on scoped deliverables or embedded with your team for the duration of a project. Most engagements run 1–4 weeks. I respond to messages within 24 hours and offer a free 30-minute scoping call before any commitment.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Biostatistics
• ☆ Bioinformatics
• ☆ Structural Bioinformatics
• ☆ Python
• ☆ R
• ☆ Technical & Scientific Writing
• ☆ Manuscript & Journal Article Writing

Services

• Writing
• Research
• Data & AI

Writing Technical Writing

Research Meta-Research, Technology Scouting, Gap Analysis, Gray Literature Search, Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Data & AI Predictive Modeling, Statistical Analysis, Image Processing, Image Analysis, Algorithm Design-Non ML, Algorithm Design-ML, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights

Work Experience

Research Scientist

National Institute of Health

January 2025 - Present

Research Assistant (Remote)

Green Biotech

January 2025 - December 2025

Technical Analyst Bioinformatician

Biocomputomics

March 2024 - July 2025

Bioinformatics Scientist

Mertech

January 2021 - January 2024

Education

MS Bioinformatics (School of Interdisciplinary Engineering and Sciences (SINES))

NUST

September 2021 - December 2023

BS (Hons) Bioinformatics (Department of Bioinformatics and Biotechnology)

GCUF

August 2017 - August 2021

Certifications

• Big Data, Artificial Intelligence & Ethics

  University of California, Davis

  https://coursera.org/verify/OMA2VX48G3MX

  January 2024 - Present

• Generative AI with Large Language Models

  deeplearning.ai

  https://coursera.org/verify/XK338H9VSHKU

  January 2024 - Present

• Data analysis with R

  Google

  https://coursera.org/verify/Z4UFZHSIFOZI

  January 2024 - Present

• IELTS Academic

  IDP IELTS Overall 6.5

  August 2024 - August 2026

Publications

JOURNAL ARTICLE

Kashif Saleem, Zubia Rashid, Hania Ahmed, Muhammad Razi Uddin Siddiqui (2026). Towards Safer Antimicrobial Peptide Therapeutics: A Predictive–Generative Framework Targeting ESKAPE Pathogens . Probiotics and Antimicrobial Proteins.

Kashif Saleem, Saima Ejaz, Rehan Zafar Paracha, Maryum Nisar, Afreenish Amir, Fouzia Parveen Malik (2026). Designing of sorafenib analogs to target c-Raf for the management of hepatocellular carcinoma: Molecular dynamics and mmPBSA analysis . Journal of Bioinformatics and Computational Biology.

Kashif Saleem, Linta Khalid, Saima Mushtaq, Iltaf Hussain, Zamir Hussain, Zainab Hussain, Rehan Zafar Paracha, Amjad Khan, Jie Chang, Yu Fang, et al. (2025). Global Prediction of Antimicrobial Resistance Trends Using Statistical and Machine Learning Models: Evaluating National Action Plan Policy Impacts Through Interrupted Time Series Analysis . Journal of Global Antimicrobial Resistance.

Kashif Saleem, Saima Ejaz, Rehan Zafar Paracha, Maryum Nisar, Afreenish Amir, Fouzia Parveen Malik (2025). Designing of sorafenib analogues to target c-RAF for the management of hepatocellular carcinoma; Molecular dynamics and mmPBSA analysis . Journal of Bioinformatics and Computational Biology.