Bilal Sharif

My principal postdoctoral project is DNAharvester, a modular and reproducible Nextflow pipeline I developed at the Centre for Palaeogenetics for analysing highly degraded DNA from ancient and historical specimens. It addresses the central bioinformatic challenges of ancient DNA, including short fragments, low endogenous content, post-mortem damage, and cross-species contamination, through metagenomic pre-filtering, competitive and adaptive mapping, and systematic evaluation of reference bias. The pipeline also includes subworkflows for mitogenome assembly, taxonomic classification, genetic sex determination, and variant calling, with the aim of making rigorous analysis of degraded DNA accessible to the wider research community.

I am a computational biologist working at the intersection of computational biology, palaeogenomics, and population genetics. I hold a Postdoctoral Researcher position at the Centre for Palaeogenetics, Stockholm University, and, since January 2026, serve as Lead Computational Biologist at GenomeVault. My research recovers biological signal from deep-time samples to study the ecology, population dynamics, and evolutionary history of species such as Homotherium latidens, mammoths, and ancient equids. I am also interested in metagenomic approaches to ancient environments and in integrating multi-omics data to reconstruct past ecosystems.

Alongside DNAharvester, I develop and maintain open-source tools for iterative mapping, adapter cleaning, capture-probe design, and SNP network reconstruction. On this site you will find my publications, a full CV, the software and repositories I maintain, and a blog on bioinformatics, ancient DNA methods, and reproducible research.

selected publications

bioRxiv
DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens

Muhammad Bilal Sharif, Verena E. Kutschera, Nikolay Oskolkov, and 8 more authors

bioRxiv, 2026

Preprint

Abs DOI Bib HTML

DNAharvester is a modular, reproducible Nextflow pipeline for processing highly degraded DNA from ancient and historical specimens, integrating metagenomic filtering, competitive and adaptive mapping, reference-bias evaluation, and subworkflows for mitogenome assembly, taxonomic classification, sex determination, and variant calling.
@article{sharif2026dnaharvester, title = {DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens}, author = {Sharif, Muhammad Bilal and Kutschera, Verena E. and Oskolkov, Nikolay and Guinet, Benjamin and Lord, Edana and Chac{\'o}n-Duque, J. Camilo and Oppenheimer, Jonas and van der Valk, Tom and D{\'i}ez-del-Molino, David and Heintzman, Peter D. and Dal{\'e}n, Love}, journal = {bioRxiv}, year = {2026}, doi = {10.64898/2026.04.20.719564}, note = {Preprint}, }

iScience

Late Iron Age and Roman equine breeding north of the Alps: Genetic insights and cultural implications

Muhammad Bilal Sharif, Azadeh F. Mohaseb, Ludovic Orlando, and 2 more authors

iScience, 2025

DOI Bib

@article{sharif2025equine,
  title = {Late Iron Age and Roman equine breeding north of the Alps: Genetic insights and cultural implications},
  author = {Sharif, Muhammad Bilal and Mohaseb, Azadeh F. and Orlando, Ludovic and Saliari, Konstantina and Mohandesan, Elmira},
  journal = {iScience},
  volume = {28},
  number = {9},
  pages = {113224},
  year = {2025},
  publisher = {Elsevier},
  doi = {10.1016/j.isci.2025.113224},
}

PLoS ONE

Environmental DNA from peck marks shows potential for non-invasive monitoring of woodpeckers

Muhammad Bilal Sharif, B. Ferry, J. Fuchs, and 3 more authors

PLoS ONE, 2025

DOI Bib

@article{sharif2025edna,
  title = {Environmental DNA from peck marks shows potential for non-invasive monitoring of woodpeckers},
  author = {Sharif, Muhammad Bilal and Ferry, B. and Fuchs, J. and Cronholm, B. and Heintzman, Peter D. and Dal{\'e}n, Love},
  journal = {PLoS ONE},
  volume = {20},
  number = {8},
  pages = {e0328831},
  year = {2025},
  publisher = {Public Library of Science},
  doi = {10.1371/journal.pone.0328831},
}

Animals

Reconstruction of the major maternal and paternal lineages in the feral New Zealand Kaimanawa Horses

Muhammad Bilal Sharif, Robert R. Fitak, Barbara Wallner, and 2 more authors

Animals, 2022

DOI Bib

@article{sharif2022kaimanawa,
  title = {Reconstruction of the major maternal and paternal lineages in the feral New Zealand Kaimanawa Horses},
  author = {Sharif, Muhammad Bilal and Fitak, Robert R. and Wallner, Barbara and Orozco-terWengel, Pablo and Mohandesan, Elmira},
  journal = {Animals},
  volume = {12},
  number = {24},
  pages = {3508},
  year = {2022},
  publisher = {MDPI},
  doi = {10.3390/ani12243508},
}