Principal Research Engineer (Sep 2020 – Present)
Bioinformatics Core Facility, Faculty of Medicine & Health Sciences, Linköping University, Sweden
Clinical Genomics Linköping (CGLi, SciLifeLab) & Genomic Medicine Sweden (GMS)
Core Focus & High-Impact Contributions
- National Consortium Leadership (GMS & Clinical Genomics): Lead developer for gms-artic (SARS-CoV-2 genomic surveillance, in national clinical production with FoHM, Sweden) and gms-nallo (long-read rare-disease diagnostics); contributing to national Data Management Plan governance. Serve as Epigenomics Technological Focus Area (TFA) Coordinator for the CGLi node within the 7-node national Clinical Genomics network.
- Client Delivery & High-Throughput Service: Serve 27+ research and clinical groups across Sweden and international institutions across Europe (Italy, Germany, Ireland, UK), North America (US, Canada), and South America (Peru). Manage automated data intake, scalable computation, and secure delivery via Agilent iLab, Fraka, and Nimbus.
- Single-Owner Scalable Pipelines (Nextflow DSL2): Architected and authored single-owner production pipelines including milou (WGBS & EM-seq methylation analysis), longvarmeth (PacBio HiFi & Oxford Nanopore structural variant detection and haplotype phasing), and nanometaepigenomics (microbiome long-read metagenomics & base-level epigenomics under nf-core submission).
- Snakemake & GPU-Accelerated Production Turnaround: Engineered high-throughput Snakemake pipelines (somatic-pb-smk, TranscriptR) leveraging GPU acceleration (NVIDIA CUDA, Clara Parabricks) on air-gapped national HPC clusters (Bianca at Uppmax, Tetralith at NSC, and Fraka server) to reduce clinical somatic/germline calling turnarounds from days to hours.
- Bio-AI, Transformers & Foundation Models: Integrating PyTorch, Hugging Face Transformers, and domain-adapted foundation models (CpGPT, MethylGPT) into the next-gen development version of methylR 2.0 for high-dimensional biomarker discovery. Developed PubMed-Searcher, a Bio-RAG and LoRA-enabled literature intelligence studio providing zero-hallucination multi-article synthesis.
- Secure Data Infrastructure: Built and maintain Nimbus, a secure client-facing clinical delivery platform (Apache2/MySQL/PHP) for sensitive genomic results. Led institutional IT review and approval under EU General Data Protection Regulation (GDPR) standards (secured 2.1M SEK in ALF infrastructure funding).
- Instruments & Multi-Omics Sequencing: Direct end-to-end data analysis from 3 on-site Illumina sequencers (NextSeq 550, NextSeq 2000, NovaSeq 6000) via Illumina BaseSpace/DRAGEN, as well as Nanopore MinION and PromethION (P2i) instruments through EPI2ME workflows and custom Nextflow pipelines.
- Compliance & Integrity Framework: Built quindecagon — a CAP NGS Checklist-aligned and HIPAA Security Rule-compliant pipeline integrity framework featuring 15 automated security scanners, published on PyPI with GitHub Actions CI/CD integration.
- Regulatory IVDR Initiative: Contributing to an ongoing Genomic Medicine Sweden (GMS) initiative evaluating IVDR (EU In-Vitro Diagnostic Regulation) compliance for clinical bioinformatics pipelines.
- High-Performance Computing Administration: Primary investigator and system administrator managing 4 consecutive annual NAISS (fmr. SNIC) allocations (Bianca, Tetralith, Uppmax, PDC), managing multi-node SLURM clusters, Nautilus Linux server, and container infrastructure across production and development environments.
Postdoctoral Fellow (2017/06 – 2020/08)
Department of Clinical and Experimental Medicine, Linköping University, Sweden
Key Responsibilities
- Computational analysis of whole genome (RRBS)/ array based (450K/850K) DNA methylation analysis from
different participants in Sweden and Peru.
- Develop analysis pipelines to identify differential methylation patterns in different groups of
dataset.
- Develop pipelines with unsupervised analyses like Multi-Dimensional Analysis (MDA), Principal
Component Analysis (PCA), Component Analysis (CA), Multiple Factor Analysis (MFA) to reduce the
dimensionality of data.
- Pipeline development to use supervised machine learning algorithms (LDA, GLMNET, RandomForest) to
identify biosignature from the study.
- Develop analysis pipeline for transcriptome analysis.
- Use of MATLAB image processing to analyze live cell imaging.
Key Achievements
- Extensive use of R language.
- Develop packages in R, notes on R Markdown.
- High performance computing analyses.
- Clustering computing with R and Shell.
- Supervising 2 Ph.D. students
- Supervised (main supervisor) two master degree students.
- Co-supervised 4 bachelor and master degree students.
- Published two first authors, one shared first co-authors and two other co-authored research articles
in peer-reviewed journals.
Senior Research Fellow (2014/01 – 2017/01)
DST-INSPIRE (Govt. of India), Bioinformatics Centre, Bose Institute, India
Key Responsibilities
- Develop of analysis pipelines to identify different microRNAs (miRNAs) in human diseases and their
roles in evolutionary perspective.
- Curation of databases to develop dataset to calculate the evolutionary rates in human and orthologs.
- Linux-based approach to search sequence homology.
- Use of different programming languages like Perl, Python to analyze dataset.
Key Achievements
- Extensive statistical software analyses with SPSS.
- Develop algorithm based on shell scripts
- Linux system maintenance
Junior Research Fellow (2012/01 – 2014/01)
DST-INSPIRE (Govt. of India), Bioinformatics Centre, Bose Institute, India
- Extensive use of statistical tools, like SPSS, MATLAB. Works on MS Excel, NCBI databases.
- Use of Perl for data analysis.
- Learn research ethics, use of FAIR data and data sharing.
Institute Fellow (2010/09 – 2012/01)
Bioinformatics Centre, Bose Institute, India
- Works on MATLAB,
- Learn R and use of R packages,
WGCNA.
Research Trainee (2009/07 – 2010/05)
National Institute of Plant Genome Research, New Delhi, India.
- Molecular cloning; primer desinging; bacterial sequencing; Gel electrophoresis;
- Developed ILP markers using online bioinformatics tools.