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Abu Bakar Siddique

Abu Bakar Siddique
Bioinformatician at SLU Bioinformatics Infrastructure (SLUBI)


Abu is the bioinformatician at SLUBI, an infrastructure that provides support and training in bioinformatics for researchers at SLU.



  • Analysis of High-Throughput Sequencing RNA-Seq Data (PhD course)
  • Genome-wide predictions in breeding: genotype-phenotype associations and genomic selection (PhD course)


Metagenomics, metabarcoding, eDNA, Metatranscriptomics, DGE Mycobiome



Since June 2023  Bioinformatician of SLU Bioinformatics Infrastructure, Swedish University of Agricultural Sciences, Department of Plant Biology, NJ, Ultuna, Uppsala, Sweden

2022-2023  Forskningsingenjör of SLU Bioinformatics Infrastructure, Swedish University of Agricultural Sciences, Department of Plant Biology, NJ, Ultuna, Uppsala, Sweden

2020-2021  Post-doc research fellow (Forskare), Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden. 

2018-2019  Mobility Post-doc research fellow (Forskare), Dept of Virology, Institute Of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic

2013-2017  PhD-student (Doktorand), Institute of Botany and Landsacpe Ecology, Ernst-Moritz-Arndt Universität (Greifswald University), Greifswald, Germany

2012-2013  Research assistant (Forskningsassistent), Department of Plant Physiology, UPSC, Umeå University, Sweden




Abu Bakar Siddique (masters thesis, co-supervisor, 2021)
Anis mahmud Khokon (masters thesis, co-supervisor, 2016)
Khan  R Salehin (intern, co-supervisor, 2021)

Selected publications

  • Puthanveed V, Singh K, Poimenopoulou E, Pettersson J, Siddique AB, Kvarnheden A. 2023. Milder autumns may increase risk for infection of crops with turnip yellows virus. Phytopathology. (ja).
  • Siddique AB, Albrectsen BR, Ilbi H, Siddique AB. Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves. Applied Sciences. 2022;12(3):1136.
  • Siddique AB, Biella P, Unterseher M, Albrectsen BR. 2021. Mycobiomes of Young Beech Trees Are Distinguished by Organ Rather Than by Habitat, and Community Analyses Suggest Competitive Interactions Among Twig Fungi. Front Microbiol, 12.
  • Siddique AB. 2020. Viruses of endophytic and pathogenic forest fungi. Virus Genes. 
  • Albrectsen BR, Siddique AB, Decker VH, Unterseher M, Robinson KM. 2018. Both plant genotype and herbivory shape aspen endophyte communities. Oecologia. Mar 1:1-11.
  • Siddique AB, Khokon AM & Unterseher M. 2017. What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. 
  • Siddique AB & Unterseher M. 2016. A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition. Fungal Ecology, 20, 175-185.

    My full publication list is available here 


Bioinformatician at the Department of Plant Biology
Postal address:
Inst för växtbiologi, Box 7080
750 07 UPPSALA
Visiting address: Almas Allé 5, BioCentrum, Uppsala

Publications list: