SRI HARSHA MEGHADRI

PhD Candidate, Computational Biology

Hannover Medical School (MHH), DZL-BREATH, Hannover, GermanyJan 2020 – Present

DZL-BREATH is the Hannover site of the German Center for Lung Research (DZL), Germany's national network for translational research on chronic lung disease.

• Single-nucleus atlas: Lead computational analyst on a 150,000+ nucleus snRNA-seq dataset (10x Flex) of pulmonary arterial hypertension versus control lung; identified three previously undescribed cell populations, including an EndoMT-associated transitional endothelial state (manuscript in preparation).
• Regulatory programmes: Inferred the transcription factor networks behind the disease-associated populations with pySCENIC regulon analysis.
• Spatial validation: Implementing Xenium spatial transcriptomics workflows to localise the new populations in intact lung tissue.
• Methods: Developed a framework that extends cell-type-specific pathway analysis to bulk RNA-seq through deconvolution (first author, bioRxiv 2024).
• Drug repurposing: Ranked candidate small molecules for idiopathic pulmonary fibrosis using L1000/Connectivity Map perturbational signatures.
• Knockout model: Led the transcriptomic analysis of Serpina1-deficient mice, including pathway enrichment and STRING network analysis (first author, Int. J. Mol. Sci. 2022).
• Pipelines: Built reproducible, version-controlled Nextflow and R pipelines for snRNA-seq and bulk RNA-seq processing.

Transcriptomics Product Owner (Remote)

newGenia AB, Stockholm, SwedenFeb 2021 – Present

Pre-seed startup building a cloud-based clinical RNA-seq diagnostics platform ahead of clinical deployment.

• Platform roadmap: Own the roadmap for a Nextflow DSL2 RNA-seq platform on AWS covering STAR alignment, GATK variant calling, DESeq2 differential expression, and a module linking classified variants to aberrant expression (OUTRIDER), allele-specific expression and aberrant splicing (FRASER2).
• Technical audit: Led an audit of the differential-expression and variant-expression modules; turned findings on strandedness, reproducibility and model-formula safeguards into a 25-ticket backlog across five sprints.
• Requirements: Translate scientific and product requirements into pipeline priorities with the engineering team.

Assistant Researcher, NGS Laboratory

Sahlgrenska University Hospital, Gothenburg, SwedenJun 2018 – Nov 2019

Sweden's largest university hospital, combining clinical diagnostics and translational research.

• Platform build: Set up the 10x Genomics Chromium single-cell platform from scratch: wrote protocols, validated workflows and trained 5+ researchers in library preparation and instrument operation.
• Single-cell oncology: Applied 10x scRNA-seq to EBV-associated post-transplant lymphoproliferative disorder (PTLD) across multiple patient samples.
• Clinical assay: Designed and validated a UMI-barcoded multiplex PCR assay (SiMSen-seq) for melanoma mutation detection.
• Clinical metagenomics: Built a metagenomic NGS pipeline for pathogen detection in cerebrospinal fluid (Scientific Reports 2022).
• Library preparation: Prepared TruSeq, Ion Torrent, amplicon and custom capture libraries; ran qPCR and digital PCR; co-supervised a Master's thesis.

Earlier Research Positions

DKFZ Heidelberg, Karolinska Institute, University of Gothenburg2012 – 2017

• Research Associate, Oncology, University of Gothenburg (2017): patient-derived cancer cell lines, plasmid construction, fluorescence microscopy; survival and differential expression analysis of TCGA DLBCL cohorts.
• Research Assistant, University of Gothenburg (Sep 2015 – Sep 2016): mammalian meiosis; molecular cloning, protein purification, protein interaction assays, yeast genetics screen.
• Research Assistant, Karolinska Institute (Sep 2012 – Jul 2013): regulation of a cellular E3 ligase by an EBV-encoded microRNA (acknowledged, PLoS Pathogens 2016).
• Master's Thesis, DKFZ Heidelberg (Feb – Aug 2012): mitotic phenotypes of EBV-infected B cells using immunofluorescence, histochemistry, FACS and primary cell culture.