Abu Bakar Siddique — Bioinformatician & Molecular eologist

ProfileBioinformatician, SLUBI

Bioinformatics engineer with a PhD in molecular ecology and thirteen years turning raw sequencing data into published results. I work on the analysis side of SLU's bioinformatics infrastructure (SLUBI): consultation, pipeline development, and training for research groups across the university.

My delivery record spans 31 completed omics projects — nine amplicon studies (ITS, 16S, 18S, COI), three shotgun metagenomes, eleven bulk RNA-seq and one metatranscriptome analyses, six de novo genome assemblies with the Earth BioGenome Project workflow, and a QTL-seq study. I execute these as reproducible, version-controlled Nextflow/nf-core and Snakemake workflows on SLURM clusters, and I teach the same practices to PhD students and staff.

I pipetted before I programmed: DNA/RNA extraction, PCR, cloning, and Illumina library prep came first. That means I read QC failures as experimental problems, not just as numbers, and I can advise on sampling and library design before a run rather than after it.

ExpertiseWhat I am hired to do

Workflow engineering	Nextflow & nf-core (rnaseq, mag, ampliseq, metatdenovo, bacass), Snakemake, Bactopia, Earth BioGenome Project, pipeline design and automation
HPC & systems	Linux/Unix, Bash, SLURM, job arrays and parallelisation, SSH/rsync/tmux; NAISS — UPPMAX, PDC Dardel, HPC2N (6+ yrs)
Metagenomics	Amplicon, shotgun and long-read metagenomics; MAG assembly, binning, refinement and dereplication; taxonomic and functional profiling
Transcriptomics	Bulk RNA-seq, metatranscriptomics, QC, alignment and quantification, differential expression, GO/KO enrichment, batch-effect control
Genomics	HiFi, Hi-C and Iso-Seq assembly; scaffolding, polishing, QC and annotation; pangenomes; mitogenomes; variant calling and QTL-seq
Programming	Python (pandas, NumPy, SciPy, scikit-learn, Biopython), R (tidyverse, phyloseq, vegan, DESeq2, lme4, patchwalk), Bash, SQL
Reproducibility	Git/GitHub, Docker, Singularity/Apptainer, Conda, Pixi, Quarto, R Markdown, Jupyter; SRA/ENA/Zenodo deposition
Statistics	GLM/GLMM and mixed-effects models, compositional data analysis (CLR/ILR/Aitchison), PERMANOVA, TUKEY test, ordination (PCA/PCoA/NMDS/db-RDA), network analysis
Wet lab	DNA/RNA extraction, PCR and RT-qPCR, cloning, primer design, Illumina library prep (ITS), Sanger sequencing, bacterial culturing, clonning & transformation, fungal culturing, virus isolation

Experience2012 — present

Jun 2024
— present
Current

Bioinformatician — SLU Bioinformatics Infrastructure (SLUBI)

Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala

Serve as the analysis lead for metagenomics, metatranscriptomics and RNA-seq within SLUBI, the infrastructure providing bioinformatics support and training to researchers across SLU's Ultuna, Umeå and Alnarp campuses.
Consult on project design and deliver end-to-end analyses for research groups — scoping the question, choosing the method, running it on HPC, and handing back documented code alongside results.
Execute or build and maintain reproducible Nextflow/nf-core and Snakemake workflows with containerised environments, so analyses can be rerun by the group that commissioned them.
Design and teach the researcher- and PhD-level courses on reproducible research, RNA-seq, multi-omics, genomic selection and scientific data handling & visualisation.
Run bioinformatic drop-in support and troubleshooting for various projects related to HPC access, environment management, data analysis and pipeline or job failures across NAISS systems and local servers.

Feb 2022
— May 2024

Research Engineer — SLUBI

Department of Plant Biology, SLU, Uppsala

Delivered advanced analyses on metagenomic, metatranscriptomic and transcriptomic datasets for multidisciplinary plant-science and environmental projects.
Contributed the metabarcoding and eDNA analysis underpinning the 34-year airborne eDNA biodiversity study in Nature Communications (2025) and the bryophyte phenology study in Journal of Ecology (2025).
Ran the transcriptomic analyses for four virology and crop-pathology collaborations, published in BMC Plant Biology, Molecular Plant-Microbe Interactions and Phytopathology.
Introduced workflow-manager-based analysis and version-controlled code sharing to project teams previously working with ad-hoc scripts.

Jan 2022
— Feb 2022

Senior Research Engineer

Department of Ecology & Environmental Sciences, Umeå University

Provided computational support for environmental metagenomics and airborne eDNA work on the SweBITS project.

Jan 2020
— Jan 2022

Postdoctoral Research Fellow

Department of Ecology & Environmental Sciences, Umeå University

Analysed a 34-year archive of weekly aerosol filters from northern Sweden within SweBITS (Swedish Biodiversity in Time and Space), reconstructing fungal and wider biodiversity trends from airborne eDNA.
Assembled reference genomes for forest fungal pathogens and traced them through the air-filter sequence archive to establish a basis for early-warning biosurveillance.
Integrated sequence-derived community data with weather and land-use records to model seasonal patterns and outbreak risk.

Jul 2018
— Oct 2019

Postdoctoral Research Fellow — Virology

Institute of Plant Molecular Biology, Biology Centre CAS, České Budějovice, Czech Republic

Identified and characterised mycoviruses in endophytic and pathogenic forest fungi, combining dsRNA/total RNA extraction, RT-PCR, cloning and phylogenetics with expression analysis.
Investigated how viral infection alters fungal growth, and the potential of mycoviruses as biological control agents against fungal plant disease.

Dec 2013
— May 2017

PhD Researcher

Institute of Botany & Landscape Ecology, Greifswald University, Germany

Developed a cost-effective fungal metabarcoding protocol for Illumina sequencing, since adopted and widely cited as a reference method for ITS amplicon library construction.
Demonstrated strong seasonal turnover in phyllosphere fungal communities across altitudinally distinct habitats over two years, linking community structure to leaf biochemistry, microclimate and habitat.
Ran the full pipeline — field sampling, library preparation, sequencing and bioinformatic analysis — for beech and aspen mycobiome studies.

Jul 2012
— Sep 2012

Research Assistant

Department of Plant Physiology, UPSC, Umeå University

Molecular identification of fungal endophytes in European aspen; foundation for subsequent MSc and PhD work.

Family leave, approximately nine months following PhD studies (2017–2018).

DeliveryCompleted end-to-end: QC → processing → statistics → report

Class	n	Detail
Amplicon / metabarcoding	9	ITS — aspen leaf endophytes, beech leaf endophytes,rye seed & soil, seed metagenomics (empty vs. filled); 18S — arbuscular mycorrhizal fungi in environmental samples; COI — wildflower-associated terrestrial arthropods; 16S — rye seed & soil, river water (Bangladesh), human gut microbiome
Shotgun metagenomics	3	Airborne eDNA filter archive; alder leaf-litter; human gut microbiome — assembly, binning, MAG refinement, functional profiling
RNA-seq & metatranscriptomics	11	Sugar beet ×2; potato ×3; Brassica oleracea ×2; red clover ×2; bioreactor metatranscriptome; DGE, GO/KO enrichment and functional interpretation throughout
De novo genome assembly	6	Earth BioGenome Project — 4 plant accessions, 2 fungal isolates; HiFi + Hi-C assembly, scaffolding, QC and annotation
Microbial genomics	1	Bacterial genome assembly, annotation and antimicrobial-resistance determination at cow's vaginal samples
Other genomics	2	Sugar beet QTL-seq; red clover genome assembly, annotation and pangenome construction

Method development. Co-developed a low-cost, high-efficiency fungal metabarcoding protocol and analysis strategy for Illumina sequencing (Fungal Ecology 2016; Applied Sciences 2022), making large-sample mycobiome studies affordable. Data stewardship. Raw and processed data deposited to SRA, ENA and Zenodo; analysis code released via GitHub (40 repositories, including public teaching material on R, shotgun metagenomics and ITS amplicon workflows).

StackIn production use

Workflow & infrastructure: Nextflow; nf-core/rnaseq, /mag, /ampliseq, /metatdenovo, /bacass; Snakemake; Bactopia; Linux/Unix; Bash; SSH; rsync; tmux; SLURM; NAISS (UPPMAX, PDC Dardel, HPC2N); FASTQ/BAM/VCF/GFF at scale
Containers & environments: Docker; Singularity/Apptainer; Conda; Pixi
Metagenomics & microbial ecology: QIIME2; DADA2; Kraken2; Bracken; MetaPhlAn; HUMAnN; PICRUSt2; eggNOG-mapper; FunGuild; MEGAHIT; metaSPAdes; SPAdes; metaFlye; Canu; hifiasm; MetaBAT2; MaxBin2; CONCOCT; COMEBin; MetaBinner; SemiBin2; dRep; CheckM; GTDB-Tk
Transcriptomics: FastQC; Cutadapt; Trimmomatic; MultiQC; STAR; HISAT2; bwa-mem2; BBMap; Salmon; Kallisto; DESeq2; edgeR; limma-voom; clusterProfiler; GO/KO; ComBat-seq; SVA; Harmony
Genome assembly & annotation: hifiasm; pairtools; YaHS; QUAST; BUSCO; merqury/meryl; MitoHiFi; Prokka; Bakta; ANI comparison; assembly QC
Phylogenetics: MAFFT; IQ-TREE; RAxML; MrBayes; FastTree; phangorn; ape; phytools; MEGA
Programming & data science: Python (pandas, NumPy, SciPy, scikit-learn, Biopython, matplotlib, seaborn); R (tidyverse, ggplot2, ComplexHeatmap, phyloseq, vegan, DESeq2, MaAsLin2, lme4); Bash; SQL; RStudio; Jupyter
Statistics: Experimental design; GLM/GLMM/GAM; mixed-effects models; compositional data analysis (CLR, ILR, Aitchison); PCA, PCoA, NMDS, db-RDA; PERMANOVA and dispersion tests; alpha/beta diversity; bipartite and ecological network analysis
Reporting & sharing: Git/GitHub; Quarto; R Markdown; Jupyter; Shiny; Plotly; publication-quality figures; SRA/ENA/Zenodo deposition

Teaching6 graduate & researcher courses

Course	Role	Contribution
SLUBI–SIDA: Reproducible Bioinformatics, Nextflow & nf-core (researcher)	Co-instructor	FAIR principles; workflow managers; building and running nf-core pipelines; containerisation; GitHub-based collaboration
Analysis of High-Throughput RNA-Seq Data (PhD)	Co-instructor	HPC setup; nf-core/rnaseq; QC and alignment-metric interpretation; DESeq2 and GO/KO enrichment in R; biological interpretation clinics
Multi-omics Analyses of the Microbial Community (PhD)	Co-instructor	Metagenomics, metatranscriptomics, metaproteomics and metabolomics; assembly strategies; functional annotation; multi-omics integration via Nextflow
Data Handling & High-Quality Illustrations for Publications (PhD)	Lead instructor	Reproducible data management in R; programmatic dataset merging; multi-panel ggplot2 figures; DOI-based open-science sharing; one-week campus course plus independent project
Genome-Wide Predictions in Breeding (PhD)	Co-instructor	Linux and R foundations; tool and package setup; SNP calling and variant QC; GWAS workflows; genomic prediction with mixed models
MedBioInfo — Swedish National Graduate School in Medical Bioinformatics (PhD)	TA / guest	Genome-scale pipelines; statistical modelling; reproducibility; hands-on R and Bash

Supervision2013 — 2022

2022	Md Jonaid Hossain	Mentor (intern)
2021	Khan R. Salehin	Co-supervisor (intern)
2021	Master's thesis student	Co-supervisor
2016	Anis Mahmud Khokon	Co-supervisor, MSc thesis — led to co-authorship in MycoKeys (2017)
2013	One PhD, two BSc students	Project co-supervision

Education

2017

Dr. rer. nat. (PhD), Molecular Ecology

Greifswald University, Germany

Cumulative thesis: Leaf-inhabiting mycobiomes under different environmental conditions — local habitat conditions, leaf biochemistry and seasonal variations drive fungal community dynamics. Supervisor: PD Dr. Martin Unterseher. Thesis

2013

MSc, Ecology (2 yr)

Umeå University, Sweden

Thesis: The role of endophytic fungi in aspen leaves in the presence and absence of beetle damage. Supervisor: Assoc. Prof. Benedicte R. Albrectsen. Admitted with a full tuition waiver. Thesis

2010

MSc, Plant Pathology

Sher-e-Bangla Agricultural University, Bangladesh

Thesis: Efficacy of Trichoderma and selected botanicals in controlling leaf blight of mustard and disease variability of the pathogen.

2008

BSc (Hons), Agricultural Sciences (4 yr)

Sher-e-Bangla Agricultural University, Bangladesh

Publications19 peer-reviewed · 6 first or sole author, marked with a rule

2026

Roy S, Nemes K, Saripella GV, Vetukuri RR, Siddique AB, Savenkov EI. Comparative transcriptome profiling of Nicotiana benthamiana plants infected with potato mop-top virus and its mutant lacking a gene for the 8K protein underlines the role of chloroplasts during infection. Molecular Plant-Microbe Interactions 39(3):351–366. doi:10.1094/MPMI-10-25-0146-R
Kong ZH, Stangl M, Oester R, Rehnstam S, Futter M, Siddique AB, Bundschuh M, McKie BG. Medical facemask waste alters detritus decomposition and fungal communities in a freshwater pond. Scientific Reports 16:10597. doi:10.1038/s41598-026-45795-5

2025

Sullivan AR, Karlsson E, Svensson D, Brindefalk B, Lozano Villegas JA, Mikko A, Bellieny D, Siddique AB, Johansson AM, Grahn H, Sundell D, et al., Stenberg P. Airborne eDNA captures three decades of ecosystem biodiversity. Nature Communications 16:11281. doi:10.1038/s41467-025-67676-7
Puthanveed V, Sajeevan RS, Siddique AB, Alexandersson E, Joshi P, Snell P, Lennefors BL, Kvarnheden A. Transcriptomic responses of beet to infection by beet mild yellowing virus. BMC Plant Biology 25:1–17. doi:10.1186/s12870-025-07514-6
Bengtsson F, Cronberg N, Lozano Villegas JA, Siddique AB, Stenberg P, Ekroos J. Rapid shifts in bryophyte phenology revealed by airborne eDNA. Journal of Ecology. doi:10.1111/1365-2745.70180

2024

Islam MM, Deepo DM, Siddique AB, Nasif SO, Zonayet M, Hassan O, Siddique AB, Ali MA. B chromosomes in wheat: evolution, functions and breeding potential. Agronomy 14(11):2682. doi:10.3390/agronomy14112682

2023

Puthanveed V, Singh K, Poimenopoulou E, Pettersson J, Siddique AB, Kvarnheden A. Milder autumns may increase risk for infection of crops with turnip yellows virus. Phytopathology 113(9):1788–1798. doi:10.1094/PHYTO-11-22-0446-V
Nasif SO, Siddique AB, Siddique AB, Islam MM, Hassan O, Deepo DM, Hossain A. Prospects of endophytic fungi as a natural resource for the sustainability of crop production in the modern era of changing climate. Symbiosis 89:1–25. doi:10.1007/s13199-022-00879-4

2022

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 12(3):1136. doi:10.3390/app12031136
Islam MM, Deepo DM, Nasif SO, Siddique AB, Hassan O, Siddique AB, Paul NC. Cytogenetics and consequences of polyploidization on different biotic–abiotic stress tolerance and the potential mechanisms involved. Plants 11(20):2684. doi:10.3390/plants11202684

2021

Siddique AB, Biella P, Unterseher M, Albrectsen BR. Mycobiomes of young beech trees are distinguished by organ rather than by habitat, and community analyses suggest competitive interactions among twig fungi. Frontiers in Microbiology 12:646302. doi:10.3389/fmicb.2021.646302

2020

Siddique AB. Viruses of endophytic and pathogenic forest fungi. Virus Genes — sole author. doi:10.1007/s11262-020-01763-3

2019

Petrzik K, Siddique AB. A mycoparasitic and opportunistic fungus is inhabited by a mycovirus. Archives of Virology. doi:10.1007/s00705-019-04359-x

2018

Albrectsen BR, Siddique AB, Decker VHG, Unterseher M, Robinson KM. Both plant genotype and herbivory shape aspen endophyte communities. Oecologia. doi:10.1007/s00442-018-4097-3
Unterseher M, Karunarathna SC, Cruz GR, Dagamac NH, Dahl MB, Siddique AB, et al. Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) — a case study reveals clear tissue preferences and differences in diversity and composition. Mycological Progress. doi:10.1007/s11557-018-1375-8

2017

Siddique AB, Khokon AM, Unterseher M. 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. doi:10.3897/mycokeys.20.11265

2016

Unterseher M, Siddique AB, Brachmann A, Peršoh D. Diversity and composition of the leaf mycobiome of beech (Fagus sylvatica) are affected by local habitat conditions and leaf biochemistry. PLOS ONE 11(4):e0152878. doi:10.1371/journal.pone.0152878
Siddique AB, Unterseher M. 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. doi:10.1016/j.funeco.2015.12.009

Manuscripts in review and in preparation available on request. Full list via ORCID and the SLU publication database.

ResearchWhere I want to go next

Environmental metagenomics	Airborne eDNA for biodiversity monitoring and pest/pathogen surveillance; metabarcoding methodology; fungal community ecology; plant–fungi–insect interaction
Transcriptomics & multi-omics	Differential expression and functional interpretation; metatranscriptomics; integration of omics layers; machine-learning approaches to omics data
Research Projects	SweBITS (Swedish Biodiversity in Time and Space); TanAsp (aspen mycobiome and metabolites); Earth BioGenome Project assemblies; mycoviruses; beech leaf endophytes

ServiceCommunity & profession

Peer review	British Ecological Society journals; PLOS ONE; Frontiers in Microbiology
Governance	Board member, Umeå Postdoc Society, 2021
Networks	International Mycological Congress; Biodiversity Genomics; COST Actions FA1405 & FA1103; German Mycological Society (DGfM); International Mycological Society
Funding & awards	Seven competitive travel grants (~€10,000 total, 2014–2019); COST Action FA1405 Short-Term Scientific Mission grant (2017); full tuition waiver, MSc Ecology, Umeå University

Talks & CPDSelected

Talks	COST Action FA1405 annual meeting, Malta (2018); German Mycological Society (DGfM), Bernried, Germany (2016); Screening of Endophyte Functions and Diversity, Budapest (2015)
Posters	Nordic Oikos, Iceland (2020); COST FA1405 final meeting, Thessaloniki (2019); DGfM, Saarland, Germany (2014); 10th International Mycological Congress, Bangkok (2014); KBC Days, UPSC, Umeå (2012)
Training	Swedish Bioinformatics Workshop, Uppsala (2024); RaukR Advanced R for Bioinformatics, Visby (2023); NBIS Introduction to Bioinformatics using NGS Data (2022); Introduction to Python for Bioinformatics, Uppsala (2020); HPC2N & Linux, Umeå (2020); Presentation Skills for Young Scientists, Biology Centre CAS (2019); Ecological Network Analysis of Multispecies Interactions, IPB Bragança (2017); Academic Writing, Greifswald Graduate Academy (2016); Fungal Metabarcoding, Greifswald (2015)
Conferences	Nextflow Summit (2025); Breeding 360, SLU Breeding Network (2025); Biodiversity Genomics (2020, 2021, 2022)

Languages

English	Fluent — working language
Bengali	Native
Swedish	Basic
German	Beginner