Abu Bakar Siddique
Bioinformatician, Department of Plant Biology
Abu is the bioinformatician at SLUBI, an infrastructure that provides support and training in bioinformatics for researchers at SLU.
Presentation
Background
- Since June 2023: Bioinformatician of SLU Bioinformatics Infrastructure (SLUBI), Department of Plant Biology, NJ faculty, Swedish University of Agricultural Sciences, Uppsala, Sweden
- 2022–2023: Forskningsingenjör of SLU Bioinformatics Infrastructure, Swedish University of Agricultural Sciences, Department of Plant Biology, NJ, Ultuna, Uppsala, Sweden
- 2022–2023: First Researcher Engineer (Förste forskningsingenjör), Department of Ecology and Environmental Sciences, Umeå University, Umeå, 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.t of Virology, Institute Of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
- 2013–2017: PhD-student (Doktorand), Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt Universität (Greifswald University), Greifswald, Germany
- 2012–2013: Research assistant (Forskningsassistent), Department of Plant Physiology, UPSC, Umeå University, Sweden
Research
Metagenomics
Transcriptomics
Metatranscriptomics
Mycobiome
Environmental DNA (eDNA)
Teaching
- Analysis of High-Throughput Sequencing RNA-Seq Data (PhD course)
- Genome-wide predictions in breeding: genotype-phenotype associations and genomic selection (PhD course)
- Data handling and high-quality illustrations for publications (PhD course)
- Multi-omics analyses of the microbial community (PhD course)
- SLUBI SIDA training course—Reproducible bioinformatics, best practices, Nextflow and nf-core (researcher course)
- MedBioInfo —Swedish National Graduate School in Medical Bioinformatics (PhD course)
Educational credentials
- PhD (Dr.rer.nat.), Molecular Ecology, 2017, Greifswald University, Germany.
- Master of Science, Ecology, 2013, Umeå University, Sweden.
- MS, Plant Pathology, 2010, Sher-e-Bangla Agricultural University, Bangladesh.
- Bachelor of Science (Hons), Agricultural Sciences, 2008, Sher-e-Bangla Agricultural University, Bangladesh.
Supervision
- Md Jonaid Hossain (intern, mentor, 2022)
- Khan R Salehin (intern, co-supervisor, 2021)
- Abu Bakar Siddique (master’s thesis, co-supervisor, 2021)
- Anis Mahmud Khokon (master’s thesis, co-supervisor, 2016)
Latest publication
- Sullivan, A.R., Karlsson, E., Svensson, D., Brindefalk, B., Villegas, J.A., Mikko, A., Bellieny, D., Siddique, A.B., Johansson, A.M., Grahn, H., Sundell, D., ... & Stenberg, P., 2025. Airborne eDNA captures three decades of ecosystem biodiversity. Nature Communications. 16, 11281 (2025). https://doi.org/10.1038/s41467-025-67676-7
- Puthanveed, V., Sajeevan, R.S., Siddique, A.B., Alexandersson, E., Joshi, P., Snell, P., Lennefors, B.L. and Kvarnheden, A., 2025. Transcriptomic responses of beet to infection by beet mild yellowing virus. BMC Plant Biology, 25(1), pp.1-17. https://doi.org/10.1186/s12870-025-07514-6
- Bengtsson, F., Cronberg, N., Lozano Villegas, J.A., Siddique, A.B., Stenberg, P. and Ekroos, J., 2025. Rapid shifts in bryophyte phenology revealed by airborne eDNA. Journal of Ecology. https://doi.org/10.1111/1365-2745.70180