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Swati Gupta

@swatigupta6

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I build computational omics pipelines to uncover RNA regulation, cancer progression, and spatial tissue biology.

Netherlands

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What I'm looking for

I'm looking to continue building computational omics and machine-learning pipelines that connect RNA biology, spatial transcriptomics, cancer research, and clinically meaningful disease mechanisms.

I'm a postdoctoral fellow at Radboud Institute for Molecular Life Sciences, mapping RNA modifications through RNA–protein interactions and studying their roles in disease. I build computational pipelines that integrate RNA and protein data from CLIP-seq, iCLIP2, ARTR-seq, PAR-CLIP, and RNA-seq.

Previously at VIB-KU Leuven Center for Cancer Biology, I developed and standardized omics pipelines for metastatic and pre-metastatic lymph-node niches, breast cancer progression, spatial transcriptomics, and single-cell and bulk RNA-seq integration.

During my Ph.D. at IISc, I developed an algorithm for predicting intrinsic transcription termination in bacterial genomes and created the public INTERPIN database. My work also spans RNA structure modeling, molecular docking, histopathology image segmentation, spatial gene-expression prediction, and machine learning for biological data.

Experience

Work history, roles, and key accomplishments

Current

Postdoctoral Fellow

Current

Radboud Institute for Molecular Life Sciences (RIMLS)

Jun 2025 - Present (1 year 2 months)

Investigating RNA-protein interactions to map RNA modifications and identify reader, writer, and eraser proteins. Developing computational pipelines for integrating RNA and protein data, including CLIP-seq and related methods.

iCLIP2 ARTR Seq Data Integration

Postdoctoral Fellow

VIB-KU Leuven Center for Cancer Biology

Mar 2023 - Feb 2025 (1 year 11 months)

Created omics pipelines to study metastatic and pre-metastatic niches in lymph nodes and breast cancer progression. Standardized pipelines for single-cell and bulk RNA-seq analysis, data curation, and integration.

Spatial Transcriptomics R HPC Data Curation Data Integration

Ph.D. Researcher

Indian Institute of Science

Jan 2017 - Dec 2022 (5 years 11 months)

Developed an algorithm predicting intrinsic transcription termination in bacterial genomes and created the public database INTERPIN. Conducted RNA structure modeling and docking with modified compounds.

Algorithm Development Bacterial Genomics RNA Structure Modeling Docking INTERPIN