Bioinformatics · Multi-omics
I build the pipelines that turn raw sequence into biology, from single cells to whole ecosystems.
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Peer-reviewed publications0
Open resources maintained0
Countries of research
I am a bioinformatician at the University of Tartu, where my PhD focuses on the analysis of long DNA markers for microbiome and fungal community studies. My core work covers amplicon-sequencing and metagenomics pipeline development, long-read quality control, and benchmarking of chimera-detection algorithms.
Before my PhD I worked in clinical genomics, covering single-cell and bulk transcriptomics, WGS/WES variant calling, and CRISPR-screen analysis for cancer research. I contribute to the PipeCraft2 pipeline platform and the EUKARYOME rRNA reference database, and I am part of the TREC (Traversing European Coastlines) sampling initiative.
Research
From clinical cancer genomics to continental-scale biodiversity, built on reproducible, benchmarked methods.
PipeCraft2 · EUKARYOME
Profiling microbial and eukaryotic communities from environmental DNA using amplicon (barcoding and metabarcoding) and shotgun metagenomic sequencing, built on the containerized, Nextflow-based PipeCraft2 with EUKARYOME as the taxonomic backbone.
PacBio · Oxford Nanopore
Quality-control and denoising workflows for PacBio and Oxford Nanopore long reads, benchmarking filtering strategies and their downstream effect on biological interpretation.
PeerJ 2025
Comparative evaluation of chimera-detection algorithms for long-read amplicons, resolving which approaches minimize false positives while preserving true biological signal. Published in PeerJ (2025).
10X Chromium · CROP-seq
scRNA-seq, bulk RNA-seq and CRISPR (CROP-seq) screen analysis for cancer research, including cell-type annotation, trajectory and clonal-evolution inference, and CNV detection, using ML frameworks such as scVI, TensorFlow and PyTorch.
Nextflow · Snakemake
Reproducible, containerized workflows in Nextflow and Snakemake (Docker, Singularity), deployable on HPC clusters (SLURM) and cloud (AWS), from one-off analyses to production tools used by the research community.
Nvidia Parabricks
Germline and somatic variant calling, structural-variant and CNV detection across short- and long-read platforms, including GPU-accelerated pipelines (Nvidia Parabricks) for clinical and fungal genomics.
Open, reproducible work, from pipeline platforms used worldwide to focused methodological studies.
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pipecraft2 organization · University of Tartu
A modular, containerized pipeline for amplicon sequencing and metabarcoding, taking data end to end from raw reads to community tables and deployable on HPC and cloud. I develop new modules and maintain existing workflows.
Peer-reviewed research in computational biology and environmental genomics. Full list on Google Scholar →
From clinical single-cell genomics in Siena to environmental genomics in Estonia.
Awards & honors
University of Tartu, Estonia · Institute of Ecology & Earth Sciences
Amplicon-sequencing and metagenomics analysis of microbiome and fungal community data; PipeCraft2 module development; EUKARYOME database contributions; long-read QC and chimera-detection benchmarking; member of the TREC sampling team.
Azienda Ospedaliera Senese, Siena, Italy
10X Chromium scRNA-seq & CROP-seq workflows for cancer; UMI pipelines & sgRNA identification for CRISPR screens; GSEA, CNV and clonal-evolution modeling; ML with scVI/TensorFlow/PyTorch; WGS/WES on Nvidia Parabricks.
University of Tehran, Iran
Bioinformatics instruction for MSc students; NGS theory for BSc students; practical workshops on RNA-seq and NCBI resources.
Tabriz University, Iran
Behavioral assays and tissue analysis; data analysis with Rtrack and MouBeAT.
Contact
Open to industry roles, collaborations, and consulting in multi-omics data analysis, bioinformatics pipeline engineering, and applied computational biology.
alihakimzadeh73@gmail.comTartu, Estonia