publications

2026

1. 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},
   }

2025

1. 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},
   }

2. 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},
   }

3. bioRxiv

   The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts

   B. Guinet, Muhammad Bilal Sharif, and Tom Valk

   bioRxiv, 2025

   Preprint

   Bib

   @article{guinet2025referencedivergence,
     title = {The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts},
     author = {Guinet, B. and Sharif, Muhammad Bilal and van der Valk, Tom},
     journal = {bioRxiv},
     year = {2025},
     note = {Preprint}
   }

2024

1. Bioinformatics

   Unravelling reference bias in ancient DNA datasets

   Stephanie Dolenz, Tom Valk, C. Jin, and 4 more authors

   Bioinformatics, 2024

   DOI Bib

   @article{dolenz2024referencebias,
     title = {Unravelling reference bias in ancient DNA datasets},
     author = {Dolenz, Stephanie and van der Valk, Tom and Jin, C. and Oppenheimer, Jonas and Sharif, Muhammad Bilal and Orlando, Ludovic and Heintzman, Peter D.},
     journal = {Bioinformatics},
     volume = {40},
     number = {7},
     pages = {btae436},
     year = {2024},
     publisher = {Oxford University Press},
     doi = {10.1093/bioinformatics/btae436}
   }

2. bioRxiv

   Unraveling Genome- and Immunome-wide Genetic Diversity in Jaguars (Panthera onca): Implications for Targeted Conservation

   R. Meißner, S. Winter, J. P. Elbers, and 5 more authors

   bioRxiv, 2024

   Preprint

   Bib

   @article{meissner2024jaguar,
     title = {Unraveling Genome- and Immunome-wide Genetic Diversity in Jaguars (Panthera onca): Implications for Targeted Conservation},
     author = {Mei{\ss}ner, R. and Winter, S. and Elbers, J. P. and Pl{\'a}{\v{s}}il, M. and Futas, J. and Mohandesan, Elmira and Sharif, Muhammad Bilal and Burger, Pamela A.},
     journal = {bioRxiv},
     year = {2024},
     note = {Preprint}
   }

2022

1. J. Archaeol. Sci.

   Ancient DNA refines taxonomic classification of Roman equids north of the Alps, elaborated with osteomorphology and geometric morphometrics

   Muhammad Bilal Sharif, Azadeh F. Mohaseb, M. I. Zimmermann, and 4 more authors

   Journal of Archaeological Science, 2022

   DOI Bib

   @article{sharif2022romanequids,
     title = {Ancient DNA refines taxonomic classification of Roman equids north of the Alps, elaborated with osteomorphology and geometric morphometrics},
     author = {Sharif, Muhammad Bilal and Mohaseb, Azadeh F. and Zimmermann, M. I. and Trixl, S. and Saliari, Konstantina and Kunst, G. K. and Mohandesan, Elmira},
     journal = {Journal of Archaeological Science},
     volume = {143},
     pages = {105624},
     year = {2022},
     publisher = {Elsevier},
     doi = {10.1016/j.jas.2022.105624}
   }

2. 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},
   }

2020

1. Ann. Bot.

   Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)

   Muhammad Bilal Sharif, Concetta Burgarella, F. Cormier, and 4 more authors

   Annals of Botany, 2020

   Bib

   @article{sharif2020yam,
     title = {Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)},
     author = {Sharif, Muhammad Bilal and Burgarella, Concetta and Cormier, F. and Mournet, P. and Causse, S. and Van, K. N. and Cha{\"i}r, H{\a}na},
     journal = {Annals of Botany},
     volume = {126},
     number = {6},
     pages = {1029--1038},
     year = {2020},
     publisher = {Oxford University Press}
   }